Kitty Pride is such a flat character (and I'm not talking about her body). She has NOTHING interesting about her other than her powers. If you read Ultimate X-Men you know a little about her past, but for the most part she has no real depth.
Mary Jane, on the other hand, has all sorts of problems. I feel like I know her personally. I think the main reasons for this is that a) Ultimate X-Men has so many "main" characters that there's not as much room for character development as there is in Ultimate Spider-man and b) Bendis is a "talking-heads" style writer who's stories tend to be dialogue based instead of action based (not to say there isn't plenty of action, just that there is a lot more talking).
POTENTIAL SPOILER!!!
I think that now with it being revealed that Spider-man is dating Kitty Pride, it would be more or less impossible for Peter to maintain that relationship. I think Peter wants to live a normal life as well, and considering that any serious relationship is a major part of a person's life, for him to have that part of his life so closely tied in with Spider-man... I don't know.
To me it seems that Kitty Pride is a good match for Spider-man, but Mary Jane is a good match for Peter. It all comes down to whether or not Peter Parker/Spider-man wants to primarily be a super hero or a normal man. This theme is explored all the time is Ultimate Spider-man, whether it's Peter contemplating giving up being Spider-man, or Peter putting on the costume when his real life is being to stressful.
Sorry for the rant, my vote goes for Mary Jane, she's a classic, and Kitty is too static.
