Sure, if you go Yes Man you might be still be a House-style autocrat in the short term, but if you were so inclined, you could conceivably begin to steer the Mojave towards responsible self-government though, as Arcade tries to do in some of his endings.
That's nice and all, but generally these things don't work out so well. "Responsible" self-governing doesn't really exist imo because someone will always try to take total control of some small faction and turn it into something corrupt. Then they'll try to take more power and cause more problems. Also, Vegas is
always going to be the most powerful and wealthy section of the Mojave, so while Novac might self-govern itself pretty well, the Strip families will probably try to take more power by stealing from smaller settlements, rigging all of the gambling games, using force to threaten people, et cetera. Then there's the question of what to do with Yes Man. He'll still only listen to the Courier unless the Courier tells him to listen to someone else, so wouldn't that still make the Courier the most powerful guy in the Mojave (in other words it still boils down to the Courier replacing House)? If you say that the Courier should use his power to keep the families in check, then, well, you just have another Mr. House.
This is a good point. Yes Man is so deferential and non-threatening for the duration of the game that I forget about his assertiveness upgrade at the end. Probably the most persuasive argument against the Yes Man ending, I think.
Actually, the devs said a little while back that the "assertiveness upgrade" wasn't supposed to suggest that Yes Man was going to start acting on his own and carrying out plans himself. It was only there to suggest that Yes Man won't let just anybody who happens to be in the Lucky 38 walk up to him and tell him what to do; he'll only listen to the Courier unless the Courier tells him otherwise. So basically it just means that someone can't do to you what you did to Benny.