Pokemon is definitely the franchise that makes the larger income of the two. I think it manages to appeal to a much wider demographic than Yu-Gi-Oh is capable of doing. Not to mention that since the late 90's Pokemon has been a
very mainstream series internationally. Heck, there's even a company called "The Pokemon Company" for a couple years now.
Despite that though, in my personal opinion I like Yu-Gi-Oh more. The creatures featured in it are a lot cooler, the plots and characters are a lot darker and the other forms of media (anime, trading card game) surrounding the original manga I still find entertaining and fun.
Don't get me wrong, I still like Pokemon. I'm never going to drop it completely. It's just I only really ever buy a single game version for each new generation anymore since the Diamond & Pearl games. I've given up on the other forms of media too.