Yes Man is freedom without responsibility. It's outright anarchy that can only be contained by someone more ruthless than everyone else trying to claw their way to the top, and god help you if you're one of the poor ignored SoB's caught in the crossfire. NCR is freedom within the constraints of Law and Order. You're free, but there's duties and responsibilities that come with it. You will be safe and fairly treated however, so it's a pretty balanced deal.
If you upgrade the Securitrons, this is completely *not true.* According to my ending, at least, the Securitrons safely put down any and all instability with a minimum loss of life. Likewise, that was the whole point of Yes Man's quests - to remove any and all threats to your reign and make sure that the Strip is stable with the Three Families under you control and the enemies to your reign weakened.
My Courier, at least, eliminated the Fiends (which the NCR couldn't do) and the Powder Gangers (ditto). Likewise, they encouraged the Khans to LEAVE the Mojave which results in Wyoming becoming stabilized as opposed to being a lawless Wasteland. Throw that in with defeating the Legion and that goes a long way to bringing peace the region.
(Really, allying the Khans with NCR is a short term benefit that does long-term harm since Wyoming becomes a paradise thanks to the Khans merging with the FOA)
Yes Man is hardly the better ending. It may be better in the short term, when people are flush with victory and happy, but after that things will quickly go to hell unless the Courier really steps up.
The game's sidequests I think are where the decision is mostly made. Without doing the sidequests, NCR is effectively going to be gutted badly as much as if the Courier doesn't upgrade the Securitrons as well as doing none of the sidequests. McCarran horrifically damaged by the Fiends, Camp Golf slaughtered, the Strip hit by Omerta attacks, The Kings going to war with NCR's troops (presumably more rioting than outright war), the Khans on Caesar's side, etc. etc.
Really, NCR only "wins" at Hoover Dam because of the Courier.
Besides, it's not like NCR got the worst out of the deal if the Courier goes Yes Man either. They get a (possibly) peaceful withdrawal, a buffer state, and a new trade partner.
The NCR ending though, brings in an already tried and capable government, a battle hardened army, and established trade routes. It may not be the freewheeling "freedom" of the Yes Man, but it's sure as hell better than a lawless region where only the strong can survive.
Again, if the Courier doesn't go to MAMMOTH lengths to resolve their problems, NCR's army is gutted and blasted by the Legion and their defeat is at a ridiculously high price. All of the same good that the NCR is allowed to benefit from is available in the Yes Man ending. Likewise, the lack of taxes on New Vegas as well as the Securitrons will provide Vegas with an exceptionally powerful skilled military as well as a huge starting "seed" fund for building up New Vegas' infrastructure.
A Good Karma Courier will have a slightly more chaotic Wasteland but not one necessarilly where things are bad. All of the towns I dealt with, for example, were propsering.
(Goodsprings especially)
What seems most natural to me would be the House ending, because it's a bit strange hearing a story about a courier getting shot in the face, then saved by a robot belonging to Mr House. (well, "sort of" belonging to him)
I think it makes thematic sense because you realize Benny is just a pasty and the real person responsible for you getting shot in the head is effectively the man who set up the situation in the first place. Mister House rescued you but only because he wanted you to be his lackey and get him back his chip. In the end, you killing House pretty much frees you from the scheme where you were nearly killed for his greed.
No, House isn't evil, but him winning means Vegas will essentially be a nation of slaves.
A snowglobe if you will with him as their Tin God. A benevolent Tin God? Yes. But it's the same reason I hate the Calculator ending for Fallout Tactics.