jbevermore
Warmongering Menace
It is true that they are more "different" than Civ teams, but I don't think that the only way you can get that is by handing out negatives. What if Morgan had say, +4 Economy and +0 Environment (or whatever the attributes were called, can't remember), and the Gaians had +4 Environment and +0 economy, instead of -2/+2? You'd of course have to balance out with the other "civs," but the point is that you could do the same thing without handing out penalties.
They could give the current civs more extreme abilities if they wanted, but maybe they felt that those fit more in a scifi environment than in one that is historically-based.
I'm neither for nor against penalties, but I think that it's silly to say that a game that uses more penalties is more "complex," emphasis on the quotation marks.
EDIT: taking away the negative modifiers in the example above also doesn't mean that there aren't negative consequences in taking one of those factions over the other. The same, very real, choices are still there.
If you take away the negatives, it's just an opportunity cost like TMIT was saying. Part of what was interesting was those negatives, sure going all out on econ could make you crazy amounts of money but you risk an environmental meltdown if you push to hard (again for those that haven't played AC, +2 ECON meant +1 money on EVERY TILE throughout your empire. Bad environmental penalties meant randomly spawning hostile units). So the bonuses could be huge, but the penalties could be equally bad.
I'm not suggesting that Civ should just mimic what AC did, I'm simply making the case that negative modifiers (carefully used) are not a penalty to fun. Far from it, when done right they can really make those "interesting choices" that Sid Meier talks about interesting.