X-Men was better because it supported six players, but I felt the enemies were more monotonous- all the different colored foot soldiers with different weapons in TMNT beat out the sentinels in X-Men. I loved the ability to attack grounded enemies in X-Men though.

All in all, I would say TMNT was a better game. It certainly had more legs, spawning similar sequels up to the present day Shredders Revenge.

For superhero specific beat em ups, I would take Captain America and the Avengers over X-Men as well. It's got a very strong comic book feel, and the announcer yelling "America still needs your help!" when you run out of lives is classic.