I side with Mr. House 90-95% of the time and with the Legion for the remainder. House and the NCR both have fully fleshed-out story lines, Yes Man's is deliberately sparse because his questline is designed to be completable no matter what, as a failsafe against softlocking the main questline. The Legion is a great meme but they only have about two side quests you can do (Lucius' quest to fix the howitzer and Vulpes' quest to protect his spy on the Strip and help another of his spies at Camp McCarran) because they apparently decided to implement them last and were running out of time.
The NCR sucks, not just because it's Tandy's personality cult, not just because it's incompetent and horribly corrupt, but because they aim to restore all of pre-war society, even the really bad parts, because they have learned absolutely nothing, (Fantastic's dialogue at Helios One reveals that the madmen actually decided to revive the universities. Glory to Caesar for opposing them.)
Yes Man sucks because once you win, he reveals that he's going to go offline for a while to upgrade himself to be more assertive. (I know Josh Sawyer says you didn't just put Skynet into power and that he's upgrading himself so he can only serve you and not just anyone who gains access to him, but that sounds like Ridley Scott's after-the-fact editing of Blade Runner to remove anything that suggests Deckard isn't a replicant.)
So I pick House most of the time for a full experience, and do a Legion run whenever I feel like selling Arcade Gannon into slavery for the dual crimes of being gay and of being Reddit incarnate.
In the end, the only bad choice is letting Cass and Arcade live to the end credits, because they're Chris Avellone's and Josh Sawyer's mouthpieces, respectively, and they absolutely won't shut up. (Speaking of overstaying one's welcome, note that if you do any of the DLCs, be sure to quicksave as soon as the intro and outro cutscenes play because they're all unskippable and way too long, and the last thing you want is for the game to crash and have to sit through one twice.)