I'm something of a connoisseur of fighting games, and I gotta be honest; they're both excellent, and I think you'd probably have a great time no matter which one you ended up choosing. They're both fairly easy to pick up and play while also boasting leagues and leagues of technical depth, they're both bursting at the seams with content (perhaps slightly less so in MvC3's case), they both have thriving communities, both online and off. You can't lose.
Really, it comes down to what your taste in fighting games is like. The Marvel VS games are fast-paced and frantic, and MvC3 is no different; it's the kind of game where stuff is flying across the screen every second. Everything is very fast and over-the-top, sometimes to its detriment (in my opinion, anyway). Ultimately, the ability to keep up with that manic pace and do a lot of moves very, very quickly is the key to success.
Mortal Kombat, on the other hand, plays at a more traditional, measured pace. The fighting is much slower than what you'd see in Marvel, though certain features like tag-team and X-Ray Moves do speed things up a little. Unlike Marvel, high-speed combos aren't really the be-all-end-all lifeblood of this game. It's more about placement and precision, making the right move at the right moment.
So yeah, I know this has been kind of rambling, but I hope you find it useful.
