House. House is predictable. You know what he's ultimately all about, everything he does is linked to making a profit, and he doesn't pretend otherwise. You can trust he won't necessarily oppress people, or muscle in on someone else's turf (like some of the OTHER factions), because for his enterprise, those aren't really profitable ventures. And in the process, he will bring a semblance of safety and security to the Mojave. He can be pretty ruthless when dealing with others, but if people won't listen to your words while holding the big stick, well, you have no choice but to use said stick. And he's up-front about his rules, which are in turn pretty lax, so you're not really going to be losing a lot of liberties anyway. He taxes heavily, but then, so does the NCR, but unlike them, he's more likely to keep his end of the bargain and keep you safe. And if you still don't like living under him, well, his territory is thankfully going to remain small.
Will his pet projects work? Doesn't matter. If they do, fantastic, humanity can see advancement, and make moves to get off this irradiated rock. If they don't, oh well, at least he'll have made many scientific discoveries in the process, and put a lot of people to work. Seems a win-win situation.
But most of all...House is just one man. If he ever oversteps his boundaries, in one way or another, he can be...dealt with. Pull the plug on him, raze the 38 to the ground, whatever. And the Courier is in the best position to keep him in check. The same can't be said for Yes-Man. As long as there are Securitrons, as long as that program that replicates him is there, he'll always exist, the only way to defeat him would be to effectively destroy Vegas and every last Securitron, and don't expect Vegas or the Mojave to keep its sovereignty for long should that happen.
I think one of the biggest issues for me in this game is House. Like, if I look at the (very VERY little) info provided on him, I see no reason to hate him or fear him. I always feel like I'm missing something when the NPCs say "god I hate that damn House," because they never actually justify it. He demands control over Vegas and he demands cooperation from his "employees." Yeah ok, and? If tomorrow, some random dude forced himself into office as the new president, I'm sure we'd all be ticked. If after 4 years though, we figured out he was pretty level-headed...well then why would he deserve death?
I think what people take issue with is his hostile takeover of the Strip seven years prior. We do know that many people died in the process, and he has since been seen as a usurper and tyrant. They may have a point, but ultimately, yeah, I'm with you. What he did really isn't all that different than what warring tribes do anyway; he just happened to have the biggest baddest "tribe" of them all. But all accounts point to House being an "ask questions first, shoot later" kind of guy (provided he doesn't already know that you're irreconcilable, like a certain Brotherhood); he wants people to submit to his rule. If they don't, and they refuse to budge or respond with violence, well, he's gotta' enforce his claim. Personally, I think that's what happens to the Kings in most of the endings; House moves into Westside and makes his demands. And the Kings, being what they are, refuse and fight back, not knowing or caring that they're clearly outmatched.