NCR: I've sympathized with the NCR since FO2 (and before when they were just Shady Sands in FO1) because they represent a return to the old world and things like democracy, order and so on. Still, corruption flourishes and brahmin barons run the show while the people's best interest is oversighted. To expand NCR sometimes does dirty things... Specifically concerning the Mojave, I think they outstretched themselves out of ambition: more lands, the eletricity of Hoover Dam. While I'm not naive enough to believe they're there to free the people and protect them from the Legion, I can see some advantages to NCR rule IF they can keep the their grasp of the land and effectively occupy and defend it
Mr. House: the man is a genius, there's no denying it. If not for him, the Mojave would be much more devastated than it is (thanks to his anti-missile system). He claims he can restore the technological marvels of the old world in some decades. But he doesn't care about what people want or what may happen to some of them for him to achieve his goals. He's some kind of white dictator, preferring to use manipulation over brute force (but not discarding it - just look at the Securitrons). If I were to put him in charge it would be for the beneficts of a technological renaissance he would bring.
Independent Vegas: this option appeals to me because I believe in self-determination. Plus it would mean a Vegas safe (for a time at least) of the threat of the Legion and free from the rule of NCR. It would be a lesson to the NCR about how they annex new territories, that they should listen to what people say and not simply roll over them and drop laws and taxes on their heads. It would put Vegas in a better position to negotiate a future annexation to the NCR - or maybe simply an Alliance. On the downside, it would case chaos in the area and many groups with less-than-honourable intentions would take advantage of the situation.
Legion: I don't like the Legion... they're slavers and totally brutal. Even if Caesar has some interesting ideas and plan to reform humans to his ideals his methods are simply unforgivable. The trade-off between order and lack of freedom he offers is simply not good enough
So what do you think about this? What faction you supported and why?