"the best option is to put Yes Man in charge."

I have to disagree there. An independent New Vegas is probably the worst if we're talking about the future of the Mojave. With Yes Man in charge there is no growth, no structure. Once you die, then what? Yes Man can't run the country on his own, after all. The Legion provides an excellent short term rule, but their reliance on slaves, tribes, and Caesar all show just how weak they are internally, once Caesar dies(naturally, I'm going to ignore the Lanius for now) then they'll lose their one binding force. Eventually all the female slaves they take in would probably rebel, weakening it even further into the Legion slowly dies off, just like the real Rome. Sure they offer excellent protection but the NCR does too, at least they do in California. The NCR offers exactly what the Legion offers in their own borders, they're just stretched a little too thin right now to do it. And the taxes are to be expected, they're growing as a nation and need the capital to do so, so they'll probably even out later. However, the NCR does have a lot of initial problems right away and their democratic system slows them down, but all in all they're basically just the inverse of the Legion; they offer long term stability rather than short. If there was an objective best, I'd probably be Mr. House. Someone below mentioned how Yes Man could just use data on Mr. House's plan to grow, but he's human and it's a big "if" about whether or not he saved his "Save Humanity Plan" onto actual data. Then there's also the fact that if Yes Man takes the "Save Humanity Plan" that I'd no longer be flexible and respond to problems that arise in-between, so I doubt Yes Man could efficiently do what Mr. House planned on doing. Mr. House is also a brilliant man, he even stopped the destruction of New Vegas by reading the flow of war and planning accordingly. "With all that money pouring in? Give me 20 years, and I'll reignite the high technology development sectors. 50 years, and I'll have people in orbit.100 years, and my colony ships will be heading for the stars, to search for planets unpolluted by the wrath and folly of a bygone generation." Mr. House is the only one who actually has a plan for the development of society again, he's the best planner, and he's incorruptible. There's really no story reason to not pick Mr. House, he may be a little apathetic towards others but it's for the sake of progress. Every other faction in the game doesn't even think about producing new technologies, they're all so fixated on the old world they can't look ahead and, as Dead Money said, "Let go." Their society can't progress as long as that happens, old world tech was created to solve problems within the Old World, not the New World. It's stagnation and it's also why the Brotherhood of Steel will never aid the progression of the New World, too fixated on the old and refuse to look at the new.

That being said, Mr. House isn't the best option gameplay wise. Independent/Yes Man is the best for gameplay because you don't need to destroy any faction in the process Except Mr. House while Mr. House is tied with the Legion with the worst gameplay value because you need to destroy a shit ton of factions in the process, leaving all those questlines unplayable.