You have the option of seeing a full on superheroes vs supervillains war movie OR a superhero against a non-super-powered villain rehash. We've seen it before. Sure the fx will be better, but the trailers don't feel so original. I feel like it's a been there done that kinda deal.
I choose X-3 over Superman.
I've grown tired of the Superman mythology, and love the multiple layers of the X-Men mythology. X-Men has the potential to go anywhere.
Superman feels incredibley limited to me.
I will see Superman Returns nontheless, but if I had to choose between the two, it would definitely be X-Men.