I tried out a few faction tweaks as well to go along with this:
Hive - +2 Growth, +1 Industry, -2 Economy
Spartans - +2 Morale, +2 Police, -1 Industry (I didnt want to give her more police at first, but with -2 econ on Police State now, it wont really do anything to allow her to wage war in FM because she will have 0 Econ with Police State)
Believers - +1 Probe, +2 Support, -2 Research (removed the -1 Planet, it didnt make any sense or do anything anyway).
University - +3 Research, -2 Probe (for the AI univ because thay are always too squishy, with random personalities and an Aggressive zach however, he actually managed to capture my cities on Thinker difficulty! I like aggressive Zach with +3 research

).
Morgan - As an AI he needs some kind of massive help (he is ALWAYS the weakest AI faction). But when I'm playing him, he needs a massive nerf because +4 Economy is simply the best thing you can get in the game. I didnt change him sine I am playing him, and dont really know how to fix him for the AI (+Econ is capped at +4, +5 is meant to give you +4 energy per base but it doesnt). Also, boosting his econ wouldnt help the AI, it is simply stumped by trying to handle his small base sizes and -1 support (screws him up for the AI even more than Santiago with -3 industry is, because all the AI does is unit spam). Hmmm, so maybe remove his -1 support, and reduce his base size penalty to -2 instead of -3.
Gains - No change. As an AI they are a decent mid tier faction, when played by me they pwn everything with mind worms. Once I tried giving them free recycling tanks in every base, and that simply overpowered them. Maybe something like free centauri preserves when the technology is researched will help them a bit because they never need to build these for the eco damage reduction, only for the native lifecycle bonus.
Peacekeepers - Very weak AI faction, second weakest to Morgan, with Zach normally being the third weakest. But I cant think of what to do to fix them because their bonuses arent helped by simple social tweaks.