I remember when Spider-Man had lots of good stories utilizing many supporting characters that really are no longer in Spidey's world. MJ of course, Robbie Robertson, Betty Brant, Ned Leeds, Harry Osborn, Liz Allen (although they are doing something with her with the Alchemex thing) Glory Grant, etc. So I think that the "joke" has some truth to it. MJ hasn't been utilized because of the editorial changes in later years, and now she has an interesting role in Iron Man, and hints of her connection with Peter are there too. So for now, she seems to be an IM supporting cast character, and it seems to fit.