For me, it's got to be the NCR; sure they're going to ramp up the taxes on a whole load of settlements, but they remain in charge of Hoover Dam ("as is" at the start of the game) and I don't think they're too interfering to be honest. Depending on how things play out the Great Khans remain how they were, BoS remains (semi-) how they are; most places seem like a win-win.
I guess this is obviously a bit of a spurious argument - people can say "but if you side with NCR Mr. House dies!" - to get things down to the bones what I mean is which faction leaves most minor factions close to how they were originally or not too far from their original aims. Honestly I think going independant messes things up a lot, and so do House and the Legion (House for BoS, and Legion for almost everyone) - but I'd like to hear a case made for all three.