Well, ever since Peter and MJ were married in 616, some writers must of thought that her happy-go lucky, party girl personality must have made her unlikeable, never mind that her character had considerably deepened because of writers like Marv Wolfman, Roger Stern, and Tom DeFlaco. So the powers that be at Marvel either tried to make her into nothing more than either "Mrs. Spider-Man" or your typical nagging cop's wife, who at one time contemplated an affair with a fellow actor and took up chain smoking because she didn't like her hubby being Spider-Man so much--even though that was partly why she was attracted to him in the first place. Yeah, real likeable :rolleyes. As a result, she's pretty much become the scapegoat for why Marvel believed nobody could relate to Spider-Man. Heck, one of the goals of the Clone Saga and the Reboot was to get rid of the marriage, and they failed both times. Due to the films, however, MJ has been pretty cemented the idea that she's pivitol character in the Spider-Man mythos, and, as I've said before, the treatment Peter and MJ as a couple has been one of JMS' strong points during his run.
Ultimate MJ, however, has problems of her own. One of the biggest mistakes Bendis did when he started Ultimate Spider-Man, IMO, was to make her a science whiz like Peter--even though the only thing she did to suggest she lived up to her nickname "Brainy Janey" was to read a book, was once Peter's lab partner, and try to start a study group. As a result, she and Peter were set up as being too much alike, even though the reason why their relationship worked in the original comics was due to the fact they seemed like such opposites. Bendis sort of corrected this in Ultimate Spider-Man #13 in which he balanced the sweet girl-next-door with the 616's effervescence, but then he made the additional mistake of having them become a couple, when it would've been better to tease when Peter and MJ will ever get together a bit longer. For this reason, and the constant pattern of Peter and MJ breaking up and getting back together again is why most fans welcomed a relationship between Peter and Kitty Pryde (even though I believe that, like the relationship Peter had with the Black Cat, was the wrong move for Peter to make, as it looks like we're starting to see). Hopefully, Bendis can try to play the angle of Peter and MJ as friends but are in denial of their mutual attraction now, and even better have her start dating Mark Raxton and start becoming more of a party girl in a misguided attempt to get over Peter.
Can't say much about the MC2 MJ because I haven't followed that series much (and yes, I'm really, REALLY sorry about that
) but she seems like that's what the 616 version of the character would've naturally become and at least her daughter is alive in that universe.
Surprised no one has brought up Sean McKevver's treatment of MJ in his
Mary Jane minis and
Mary Jane Loves Spider-Man. Sure, it's fluff, but the way she is portrayed in that series is, to me anyway, what Ultimate MJ should've been from the start.