Is there a way to become the leader of the Mojave. I've haerd that Yes Man ends up leaving it in anarchy.

It's not anarchy. Yes Man just yoinks control of the Securitrons out from under you and takes over. It may become more anarchic outside Vegas, but his ending says he cleans up the city itself.

As for controlling it yourself, no, you can't. It svcks, but it's also in line with the other Fallout games, where (except for that atrocious original ending in FO3 that we will pretend never existed) the main character ends up continuing the life of a wanderer.