I've had both and it's not even a question in my mind...X-Men. TF was the fastest selling modern game I have ever had. From playing it on route I though it would keep me interested in a home environment, I was very wrong. It's so monotonous it just wasn't fun to play anymore, especially after getting through Battle For Cybertron. I was done with it within 2 weeks and moved it out ASAP. TF was a great route game for me, I could play it a few times and then not need to play it for a couple months, then repeat the cycle. Now X-Men on the other hand, I had a Pro for a couple of years and only sold it to upgrade to an LE. X-Men is a great game with variety, challenge and depth that keeps me coming back for more.

Artwork - XM comic art is really nicely done. Magento may be the best backglass Stern has done.
Game Design - XM's layout and especially ruleset are much more varied and deeper.
Sound - TF's sound is actually good, especially with a subwoofer. XM has some bad custom callouts which I don't think is a big deal, but some people do.
Dots - XM has really nice custom dots. Many of TF's movie rips are hard to decipher even if you have seen the movies multiple times.
Theme - Both are great themes, but I give the edge to XM because they went comic instead of movie. Had TF been based on the cartoon, it would have been much better.
Lastibility - XM has a deep ruleset that is much more varied very challenging. TF is the same thing over and over to light modes which are all very similar and has the standard 2x multiplier for shots that other Sterns have. I had no desire to keep playing TF after a short time because of the repetitiveness.