I don't know what exact algorithm ELO uses, but I like what you're describing about it, Mole. I think 2nd place should receive a slight reward if four human players are playing, but receive a penalty if two human players are playing. i also think fourth place should get a greater penalty than third place. Does the ELO algorithm fit these criteria as well?
I believe the [modified] ELO system they use at Asobrain would work best for MULE. It does not allow a ranked game to begin with BOTS in it. The game must be started with all human players in order to be ranked. However, if someone drops from the game, they are replaced by a BOT. Unfortunately, this directly affects the possible increase or decrease in ranks for the rest of the remaining players, unless the BOT only plays 25% of the game (see below).
Additionally, I think dropout players should automatically record a loss, and replacement players (when they're supported) should not have their rank change - with an obvious exception where you're replacing yourself - then you can receive a fair ranking.
Asobrain also has a mechanism to deal with this as well. What they do is require the player to participate at least 75% of the total game time. In other words, if their connection dies or some legitimate reason they have to leave the game, they can still be ranked as long as they played the majority of the game on their own. If more than 25% of the game was played by a replacement AI, then they would not get ranked at all (and, unfortunately, the other players ranks could increase/decrease less than they would have if the human player had played at least 75% of their game).
For more information about Asobrains ranking system, check the FAQs on their web site
http://games.asobrain.com. If you like Settlers of Catan, this is a great place to play it (they call it Xplorers). If you've never played Settlers, I highly recommend you try it. It's a really fantastic board game.