I just want to start by saying that I find it very interesting how quick people are to dismiss faction x for their faults. I don't want to do any finger pointing or anything, but I was always under the impression that each faction was meant to be simultaneously a brutal and crummy place as well as glorious and amazing.
With that said, I would have to choose between the Peace Keepers, the University, the Hive, the cyborgs lead by Aki Zeta (can't remember the exact name), or the Free Drones.
I can't stand the social darwinism that is so predominant in Spartan faction life. Survivalism is cool and I strongly encourage everyone to practice survival of the fittest in real life (just don't go hurting anyone in the process), but I just know I'd be one of the many to get chewed up in the grinder for being less than perfect or, at the very least, unlucky. The Morganites are really nothing but Ayn Rand made into ones and zeroes. She was an idiot and so were her ideas. Considering just how much Morgan goes on about exploiting resources he would just end up repeating what happened on Earth in the back story. At least synthetic fossil fuels exist right? Still though, Morganite disregard for the environment would make Chiron an incredibly toxic planet even less capable of supporting human life than it already is. Not to mention their obvious intention to wage war to transfer every single resource, no matter how mundane and plentiful it is, into a Morganic citizens private property.
The Believers aint too bad but they take their (very understandable) skepticism of technology to a level that would just make me a total isolationist within Believer society. I don't exactly hate Gaians, but I'd have the same problem there as I would with the Believers; I love technology and science. I would spend way too much time attempting to engineer machinery which would be heretical in either factions eyes, thus making me an outcast. Although I do enjoy gardening so I wouldn't feel totally out of place in Gaian lands. I'm flexible on that one.
The pirates, Cult of Planet, and data hacker people all make me sick. Their essentially a bunch of selfish, destructive, and/or narrow minded wastes of human flesh. Pirates are... well... pirates. The Cult intends to pretty much destroy the human species. Even if it would be an accident that's still where they are heading, and the fact that they are so violently dedicated to their ideology makes it even worse. The hackers seem like nothing more than teenagers who just learned the definition of "liberty" and suddenly feel as if any society which has anything less than total liberty needs to be rescued. These are the only factions which disappointed me in the entire game and that's because they break the mold of every faction having a clear cut good side and bad side. These morons are nothing but bad sides.
I would love living in the cyborg society since I would love being one in real life. They appeal to my support for all things science and value in "wisdom and knowledge". That old chestnut. I would miss a great deal of being a pure human, but the cyborgs downside of being a collective thingy majigy without much free thought (due to being part computer) isn't very tough to swallow. It's an acceptable price and is arguably a good thing. The Hive... Well I would hate to be just another gear in the machine. But on the other hand I have the honour of building utopia and probably living in the closest thing humanity could ever come to utopia... even if it was built on actual blood, sweat, and tears... and bones... and flesh... and a few other things. The Peace Keepers are clearly inefficient and pointlessly stupid bureaucrats who couldn't fix a single social/economic/political issue if all of mankind depends on it (which it does in this game). But at least they have a generous amount of liberty and individualism. If you can accept the fact that social and economic progress come at a snails pace you should be fine.
Free Drones actually make communism work, and that is freakin sweet. Of course, you need to be content with the fact that you will forever live as a farmer and/or manufacturer but that isn't too bad considering it's a relatively easy life. Tough and laborious, but low stress and high in that freedom thing everyone goes on about. The only thing which would absolutely bug me is the incredibly slow technological progress. This is the thing which always annoyed me about communism; everyone is a farmer. This requires lots of time and work, time which is taken away from academic pursuits. Still though, it's not like the world is coming to an end if my computer receives a new upgrade only once every other decade.
The University, once again, tickles my fancy for all things related to Science! Unfortunately, every citizen is a potential test tube for some crazy, and likely painful, experiment. I am seriously on the fence regarding these guys simply because of that. But well, there's a good chance the experiments could actually benefit me in some way. If I forcibly had my arms ripped off and replaced with gatling guns that fire nuclear missiles I wouldn't complain... too much. Then again, if I had nuclear gatling guns for arms people would have to listen to what I say, wouldn't they?
Science rules.