MJ isn't the problem.
The problem is that they killed off his supporting cast... They had to re-write Mary Jane as kidnapped rather than dead... Aunt May they simply ret-conned her death... Harry Osborn is still dead... Gwen Stacy is still dead... All the other little run in characters have not worked, and Flash Thompson hasn't been around in years (his reappearance). Norman Osborn and Peter's relationship has been played over and over to the point of it being bland... Doctor Octopus doesn't make all that much sense of a character to begin with... Eddie Brock isn't venom anymore, etc... Hell, even with the clone saga they managed to make that entire era's worth of villains and plotlines disapear forever rather than leaving a loose string for a better writer to fill in...
They've ****ing killed off one potential storyline after another to go for the shocker death, or the reappearance of a classic villain. What about coming up with something original for once? Why not pit Spidey against someone he's in way over his head with? Someone smarter than he is, who knows how to **** with him, whose just funnier than he is, does EVERYTHING better. Something like that. It'd be great!
That's why I love Stracynski's run on Amazing from the first issue until the **** with Sins Past and The Other... Ezekiel was a fantastic new character, whom I hope manages to show up in the future, and I'm sure they'll pull out Morlun again... All of these characters were attempts at something new, and it worked. He made the supporting cast important for the first time in years. MJ was back, and had a character, Aunt May found out about him being spidey, and reacted to that, Zeke was giving him some voodoo mumbo-jumbo, and him becoming a Science Teacher helped remind everyone that Peter was smart, and the bits with his students allowed him to develop as an older person... It was intriguing, and left me very pleased with Spidey in general.
I don't like him living in the Avengers tower, but at least the characters allow for certain character interaction with previously interesting characters... Especially his relationship with Tony Stark...
Otherwise, I want him to move out. Soon. Let him be in the Avengers and have his own series separately. Batman can handle Gotham and NYC with only one or two other heroes popping up here and there.
Also: Who the **** made the Kingpin only Daredevil territory?
Honestly, I could see Harry returning. I almost hope not... But I would like to see that kind of character again.