It all depends on personal preference, really. Each faction is beneficial in different ways. Personally, I'd reccomend the NCR generally but the Legion safehouse is the best. And Mr House is a prick.NCR, you get an extra Follower, the Ranger armour is better than Centurion Armour. if you prefer Power Armour then the NCR are the only faction that lets you become allies with the Brotherhood of Steel. and they have more Quests.
or you could just go indepndant and do whatever you want.
One for each playtrough. Suddenly the game lasts trice as long.