Probably NCR.
Since I see Legion as the nation meant to rule the world everywhere I looked at the NCR all I saw was problems.
Couldn't get past it.
It felt like I was helping the world destroy itself when helping the NCR.
So it just made me feel very bad.
Sure it had more content and more quests, but at what price?
Second is probably Yes Man.
Haven't finished it but he's funny and all but his quest seems to be very "meh" and his "faction" does not have as much interesting stuff to say as House, Legion or even NCR.
Third least favorite is House.
And I enjoyed House.
I loved doing his quests even though he's a greedy, manipulative, self righteous dike.
And on fourth place is Legion.
Which is my favorite faction despite the low numbers of quests and characters.