For me, MJ hurts this game more than anything else. She should've had 1 or 2 missions max. Spidey already had Yuri to work with. If he needed a connection at the Bugle, they could have used Robbie Robertson (a very underused character). The game would have been so much better with a 616 MJ, who is managing a night club or a fashion house. She could still help Spider-man by scoping out people/places and feeding him info. There could have been a break in or something where Mary Jane grabs one of Peter's Web shooters out of a drawer and defends herself. That would have made her seem capable without turning her into a nagging superhero wannabe that constantly puts herself in peril.
I do like the idea of playing as other characters, but it could've been handled better. One Mary Jane mission, one Yuri mission, One Robbie mission. More Parker missions.