So I finished Fallout NV for the first time and I chose a Yes Man/Independent Mojave. Seemed like there was a bit of good and bad in that ending though.

So what is best for the Mojave?

Not the Legion. you'll never convince me of that in 100,000,000 years. To let them overrun the Mojave would mean death for most that live there.

My independent ending had the Boomers and the Khans on my side. I chose to upgrade the securitrons but blew up the dam to discourage NCR occupation and had my trons fight Legion soldiers only. My courier has friends in the NCR that she did not want to have harmed. Even if they did not consider her a friend afterwards. All the same she wanted them to live. The BoS took back Helios One. The town of Goodsprings prospered as did Primm. Ex NCR members found shelter with The Kings and the Fiends all but scattered to the four corners of the wasteland. I didn't like the idea of so much anarchy in the streets of Vegas but with the major policing force of NCR gone what else would have happened?

I would have been happier with an NCR ending but had accidently screwed my chances with that long before they even became available. The NCR is spread across the wastelands of the US and I truly believe they are not as evil as some of the actions of the Mojave stationed NCR soldiers would portray.

The Legion because I know it irritates you.

Honestly there is no "best" thing for the Mojave. No matter who you pick they are going to do something down the line that will cause the Mojave to be obliterated or turned into an inhospitable bed of raiders and tribes like it was after the war. But those are all possibilities and may never happen.