I voted for and tend to favor the NCR most of the time, probably because they're the most similar to the society we have in the real life, present day Western world. They value the rule of law, separation of powers, free markets, etc. At least, ostensibly, they do. But would people who've been bombed back into the stone age be ready for a return to an Old World society like the NCR? I don't know. Perhaps Caesar has a point. That's what I love about this game. Makes you think about hypothetical politics and philosophy. And I like that no faction is completely 'good' or 'evil', only different perspectives and the great writing of the game at least allows the player to understand the motives of each faction even if he's not convinced to join them. This was done almost perfectly. I would have liked to see just a little more of the positive aspects of superficially 'evil' factions such as the Legion and Enclave as well as more insight into the problems with doing things in the Followers' naive, bleeding heart, hippie way. Then it would really tie the player up in knots. No cartoon character, throwaway good or evil factions to offer an easy way out (I'm looking at you, Fallout 3!). It'd be more gray, closer to real life. Still, I can't complain much because the game got very close to achieving this and I enjoyed it thoroughly.
That said, I also like the laissez-faire individualism of the Kings and the emphasis of the Followers on a free-market of ideas. If those philosophies could be incorporated under the protection of the NCR, that'd be where I'd want to live.