Food and Energy probably should be a little more important, but the fact is that anyone can go big in Smithore, so I have no problem with its power over the 'lesser' resources.
It's not so much the issue of how much money each of the factory types brings in as where you're taking the money from and its relation to the colony itself. The fact that you MAKE money for not just yourself, but the entire colony's score when you produce smithore, but if you produce food and energy, whether or not you sell it low to be nice, or sell it high to have some vague chance at keeping up with the players who were nabbing the three-mountain plots while you were nabbing rivers and deserts, the fact is that either way you're still just taking money from another player and not positively influencing the colony score whatsoever.
A guy completely monopolizes the ore industry and he's the hero of the colony. A guy monopolizes food and energy and it's HIS fault you're all taking a trip to the debtors prison.

Even if Food and Energy are made to be worth more during the final auction phase, it would still only be for that phase, and even then they'd only be jumping up to the store's SELL value, probably. (If it was any more, then everyone would just clean out the store on the second-to-last turn, if there was anything there, just to sell it themselves) During the rest of the game, they'd still sell as abysmally low to the store as they do currently, so Ore and Cristite will still be the real money-makers, as they are intended to be.
Only difference really if this change was made would be that people wouldn't scramble to convert all of their food factories into more smithore mines during the last couple rounds, and we might see less of the attitude of "I'd rather let all of mine spoil than allow the store to keep any in stock!" ... ... except of course for the people who don't give a darn about the colony's score and just want to jack up prices for the other players. That'll still be an option, only now it won't be the only option.