The key to getting any money from critical commodities is to price as high as possible without anyone going without.  If anyone goes without the economic system will suffer and you will in turn.  You can make some serious money by price gouging and not caring if someone goes without.  This would be a perfectly acceptable if the game only relied on your individual score to determine the winner.  The game doesn't and requires that both the colony total be above a level and your score be slightly more than everyone else.  This causes an odd dynamic where you have to be careful in avoiding excessive price gouging as it will slow down the development rate of other types of production by other players.  Short sighted gains can be the downfall of an economic system.  American banking and corporatism is chocked full these kind of examples.

The store is the central issue.  It's the reason smithore is so profitable and it's the reason food and energy are not as profitable.  The store ultimately fixes the price range for goods and is unable to properly react to "Smithore Surges".  From charting the economic system, the only good that should be bringing in any real profit to the system is Crystite.  It's the only good that directly brings new money into the system independent of the store's calculations.  Food is traded for existing player funds or store funds and then consumed.  Energy is traded for existing player funds or store funds, but is then used for production.  Smithore is only traded in for store funds usually, but MULEs are then bought at the store.  The store needs to operate as a closed system, but in the case of "Smithore Surges" it becomes a new and unexpected source of new money.

So the problem isn't that Food and Energy isn't profitable, but Smithore is too profitable because of a game's logic.  The store needs to have limited funds to operate from and react to good surges by immediately dropping the purchase price when it starts to get overstocked.

There are situations though when one player hikes the price beyond what others will pay or out of range of poor players.  After selling to the hiker player, one would be rendered unable to sell to those that were bumped out of the running by the hiker.  I suppose one could just head the hiker at the pass and take the loss of possible profit, but it still seems counter-intuitive.

As for selling to the store, there are situations early in the game where it makes sense to sell to the store.  For food, it makes more sense to sell the excess to the store until food production gets more stabilized.  Since, the food at the store doesn't spoil, it allows chance production not to be wasted and available in case of an emergency.  Anything spoils shrinks the economy and can (and probably will) work it's way to screw you over.

I like price gouging, but if it puts a player at a serious disadvantage... especially the one I've been buying energy from, I tend to take the loss on the sell than the greater loss from not having enough energy for production of food.

I say just make the game very configurable and modular.  This way everyone can win.  How?  When you create a game, you choose the module or "rule set" to use.  This way everyone can choose the game they want.  Some XML configuration files here, a few image PNG's there, and a standardized API for the really insane modder, all packaged up in a zip file ready to be download and loaded by the MULE client.

The general game format wouldn't change much, but this way people can fill in the details themselves.

Just because the original performed a particular way doesn't mean it should be repeated.  I say this because a lot of "features" and behaviors in older games were usually due to technical limitations and lack of large scale and varied perspective play-testing.  I love my old games, but they all are guilty of dirty tricks, dodging design bullets, and missing gameplay foul-ups to make a critical deadline.

If you chart out the economy of the game:  Energy is the most important commodity followed by Food.

The problem with Food is that it has a fairly direct route in the game economy:  Farm -> Player Time
Player Time is important in the beginning and mid game, but wanes towards the end.  Another problem with Food is that it can be considered a critical constant component of the economy.  Purposely starting a shortage will tend to hurt everyone rather than help one person.  As with the real world, price gouging a needed economic commodity only serves to damn everyone after awhile.

Increasing the needed food may help increase the need, but food is already needed and the game currently doesn't make it easy to have and produce a large amount of it.  To increase the price the store needs to change.  The only time a farmer makes money is when the store runs out and they have the food at the ready.  Every other time they are at the mercy of the store.  The store tends to price fix too much and enforce a limit on prices.  The store needs to be a bit more competitive and be quicker to charge higher and lower prices depending on the current stocks and estimated demand.  The present formulas in the game are way too conservative.

As for Energy, it is needed everywhere, but can be produced in large amounts fairly easily.  The problem that energy is critical for production and the economy.  Prices of energy direct translate to the prices of the other three goods, since their production is dependent on the price of Energy.  You could make it so squares with higher yield potential take up more energy, but this may just cause shortages and other issues.

I have to disagree that time management is an important part of the game.  It is part of the game, but a minor part of it.  I find the time limitations to be more of a distraction than anything.  Sure, there are tense moments and the like, but these only arise when you are having to deal with more than 3 new plots of a land or shifting MULEs around.  Apart from that, most turns are fairly methodical and routine.  The time it takes for a fairly skilled player doesn't vary too much from an inexperienced player for most actions and usually not enough to completely change the outcome of the game.  The point of the game is to play the economy, improve the colony, and do better than your opponents without crippling any of them (there by crippling the colony and yourself).

People won't take more time as the turns will still be timed roughly the same and can be configurable to the players specifications.  Also, people will still make mistakes and the costs would actually be MUCH higher in an action point system.

As for playing the AI's:  Why not?  A sign of a good game is the ability to have a decent enough AI that can play it too.  And you can't always wrangle 4 human players to play all the time.

Two ways to handle this from my thinking.  One is a slight adjustment and the other changes the system greatly.

1.  Delay everyone equally.  Based on average ping times between the host and players, introduce unique and appropriate amounts of artificial lag on the input controls of the host and other players so everyone has roughly the same response time.

2.  Introduce the ability to dial in a price to "charge" ahead to before the auction starts.  When the auction starts the player's auction icons will move forward either at or 1 above another player's price.  (At or ahead depends on the rank.)  The player icon will not move pass than the dialed in price unless prompted by the actual player.

While the time based turn works well enough for human players and keeps the game from dragging out too long, it does have it's problems and inefficiencies.  One problem is that when the AI is set for quick turns, they longer seem bound by the time or food limitations and are allowed to do far more than what they would normally be allowed.

An option for an alternative game mode is to do action cost based turns.  This might case games to be longer, but would even the playing fields, improve network gameplay, and allow for more consistency.

Every action would have a cost and you would have a pool of points based on the amount of food you had in comparison to the requirement for that turn.

Actions:
Get a MULE
Get an Assay Bot
Outfit a MULE
Move to next square
Drop a MULE
Pickup a MULE
Search for the Whumpus
Assay square

A majority of actions could just cost 1 point, and it might be decided later to increase the cost of some actions.  The product of this cost based system is that AI could be improved to do algorithmic cost based decision tree searches when making decisions about what to do.  Also, it gives some of the more methodical players a less twitch and panic game.  There could still be turn timers, but it could be slightly more generous in this mode.  Also, sometimes this style of game play would actually speed up games for some groups.

I don't see the balancing or strategic value in locking out the stores.  All it tends to do is create an artificial price bubble in a market without the consent of those involved.  I'm all for price gouging a necessity when the store happens to run out, but the problem with playing that game is it has great consequences when it goes wrong.  Crystite and Smithore don't have this problem, but Energy and Food does.  The fact that both Energy and Food spoils causes a situation where you are forced to horde against your wishes.  This then causes spoilage to leak valuable commodities from the economic system and give rise to a possible nasty shortage.

The only possible way to get around this right now is sellers to never allow buyers to go above the store's selling price.  This is very counter-intuitive and just seems like a silly glitch and lapse in reasoning design wise.  Sure, locking out stores would keep prices low on necessities, but this actually hampers gameplay and punishes players for playing the economy in a game about playing the economy.  In fact, temporary store shortages are one of the few ways to make any money off of Food and Energy without damaging the entire economic system.  I want to get my money's worth, but I don't want to hamper the economic system I'm reliant upon.

If the store has a fire and empties out of food, I'm going to take advantage of the buyers bidding for food.  This is especially true for when I have a limited surplus.  I'm going to let them out bid each other for first dibs on food.  But, if a really high bidder gets all the food they want and I still have enough left over, I want to sell it to someone or even the store before it spoils.  Just because one player thought food was valuable enough to pay out of the nose through it shouldn't exclude me from selling to a much lower price to someone else, particularly if they are the main producer of energy.

In summary, it's just an artificial limitation that only serves to limit the game for players on the illusion it does some fairness regulation in a system that already has such inherit in the system.

I have to second this.  The original may have done this, but it seems more of a logic limitation or oversight than a feature.  If the store has nothing, I should be able to sell to a price players want it and then move down.  It's not only the store that is affected, but other players who aren't willing to go up to the first grab price.  Once I sell off stuff to the high bidder, I'm limited in how I want to sell the remainder.  They may be another play willing to buy higher than what the store will, but with the price gauge moved so far up, they can't buy it.  This causes an artificial limitation of the market and just doesn't make any sense.  They're my goods, I should sell them how I will.  It also makes more sense to be able to sell them to the store rather than let them go to spoilage for the benefit of the colony and setting up an emergency stock.

I mean the AI doesn't even like this artificial limitation.

Overall, this game is a very solid.  Here's a few suggestions that I'll make trying to use the best of whatever game theory knowledge I have.

Auctions - You can go up, but never go back down.  It makes sense for buyers to set their desired prices above the store when the store is out of stock.  The problem, I've seen is that sellers can't to the same after such a surge in order to sell off their remaining stock to the store's prices after the buyers are served.  So the auction needs to the ability to go both ways.  This will become more important for other suggestions.  There also seems to be no "shoving" between sellers and buyers.  The buyer shouldn't mind being shoved down in price neither should be seller being shoved up in price.  This would open up some auction warring on goods that are in short supply or have limited demand.  If I meet a price point and keep trying to go the same direction after a second, I should be able to start moving the price that way and get my product bought or sold at the price I want.

Smithore Issues - The only way I can see to fix this issue with Smithore being THE way to win the game is to change the behavior of the only buyer, the Store.  The Store is being WAY to generous about pricing which is opening some big game logic loopholes to take advantage of.  The Store needs to have tiers of prices for Smithore, depending on demand.   Also, the the connection between cost of materials and MULE pricing should be loosened greatly.  Just because they bought the parts cheap, doesn't mean they won't gouge you on the MULE prices.  They ARE the only producers of MULEs and buyers of Smithore.  So, there should be at least a 25% markup, going no higher than 50%, on the minimal price of a MULE.  Now this price could still be higher, depending on demand, but would never go below the minimum price.  When it comes to determining the prices, the Store should be the deciding factor and it's always going to come out better.  So if the Store wants to sell MULEs for 250, they'll take their markup out first, then determine the price they buy Smithore for.  Also, the Store should never undercut themselves, which they seem to do fairly often between Smithore price hikes and crashes.  There may be a need to keep track in the background how many MULEs were produced at what price of parts to prevent the price of MULEs dropping below that point, or at least until any loss is significantly made up for by profit and the "proper" demand-based price differs greatly enough.  In summary, the Store needs to be more of a money-grubbing, cutthroat bastard.

Tiered Pricing - The Store needs to have tiers of price ranges for auctions that would be active when certain quotas aren't met.  This would mostly address Smithore issues, but could also be applied to other items, too.  The Store could have 5 ranges: Emergency, Shortage, Normal, Surplus, Overload.  Each of these ranges would be based on how far off the idea stock an item is.  For example, here's the Smithore ranges based on the number of MULEs, including those that will be made with current parts.

Emergency:  Less than 4 MULEs
Shortage:  Less than 10 MULEs
Normal:  Between 10 and 18 MULEs
Surplus: Over 18 MULEs
Overload: Over 24 MULEs

The pricing for Smithore would change depending on the active tiers.  
Emergency: Nominal Price x 2^2
Shortage: Nominal Price x 2^1
Normal: Nominal Price x 2^0
Surplus: Nominal Price x 2^-1
Overload: Nominal Price x 2^-2

These tiers are seen the in auction by multiple providing auction "floors" or even a store purchasing agent that moves around depending on which quotas have been met.  This also opens up competition for Sellers in a new direction as they try to sell their goods before a particular "floor" goes away or the purchasing agent moves to the start of the new price range.  With auction shoving, this would start a war to get your goods sold before the quota goes away.

These tiers could also work both ways, hence creating new auction "ceilings" or store selling agents for buyers.  As the store drains of it's stock, it would adjust the prices accordingly.  If both these floors and ceilings or purchasing and selling agents were active at the same time with the quota ranges being able to turn on and off immediately...  Auctions would become VERY INTERESTING and open up many new gameplay tactics.  

Crystite - I think the average price needs to be raised significantly, but also the greater variance of price.  This would then make it enticing to play the Crystite game.  The risks are plenty enough, but the possible rewards just aren't enough to make worthwhile.

Land Grants - If you want something the lower right corner, you are screwed.  So, a simple fix is to allow a second pass if someone hasn't selected land yet.  That way if you get jumped for something the lower corner, you'll get another pass.

AI - The main problem I have with the AI is that is doesn't seem to factor in the budget and market to it's actions.  I've caught it trying to do something without next to no time left, attempt to purchase a MULE with no money and get stuck, get a MULE but have no money for a kit and get stuck, or pay ridiculous amounts of money for MULEs and kits to enter a flooded market.

Whumpus - The "hit zone" needs to be enlarged slightly.  It's pretty annoying to waste time by only being a few slight pixels off in some indeterminable direction.

Well, that's all I could come up with at the moment.  Hope my inane ramblings help ya'll out.