You know what? Just read any of my other rants on this subject, it's pretty well covered there.
However, the short version.
Mary Jane is:
-compatible with Peter because they've both had to make difficult choices about responsibility, they both have a biting and wicked sense of humor, and they even so much as have some common interests.
-a character in her own right, and not just support
-someone who uses her 'fun' persona to mask her own problems and insecurities
-aware of what Peter does and that he does it not out of some obsession with trying to fix the past or atonement.
-sees a woman who is so many things at once and balances them all in a way that takes so much effort for him
-doesn't have one tenth of the ability to be as comfortable in his own skin as Mary Jane does
-knows that Mary Jane is the stronger one because of all this, and inspires him to try to do better
Done for now.