After everything I've been through in the Mojave, I've come to realize that everyone - NCR, Legion, and House - are all to incompetent to be able to run New Vegas to the largest amount of the population. I've never picked the Yes Man ending, because I can't find a way to justify anarchy. Are there any choices I can make with Yes Man that can ensure a good ending for the majority of the Mojave?
Try to get the best outcome for every settlement/group while maintaining their independence.
Keep the NCR as your friends by helping them out in their war effort against the Legion. If you are in good standing with the NCR and aren't detected planting the chip on the power substation you only need to convince the NCR to back down (the Boomers with bomber can help with that).
"Destroying" the Powder Gangers and the Fiends is a must. Deal with Tabitha and the Khans how you see fit, but deal with them. It's probably better to destroy the Brotherhood, though with McNamara at the head you could let them be if you don't want to kill them.
Despite all of this the departure of the Legion and NCR does attract some more raiders and bandits. Though the towns do prosper and are capable of defending themselves.