The Lana/Lois dynamic in Smallville is another great example of what the Gwen/MJ dynamic should be on film. 
Gwen is a girl. She's representative of Peter's innocence, youthfulness, and naivete. She and Peter are almost like Romeo and Juliet. They are star-crossed lovers whose immature teenage love affair is tragically cut short before it can blossom into a mature adult relationship. Webb perfectly captured that naivete in Peter breaking the promise that he made Captain Stacy. 
But Mary Jane is a WOMAN. Regardless of her age, there's a sexiness, a maturity, a confidence, and a worldliness in the way that she carries herself. She's gone through a lot of crap in her life (had to grow up quickly) and it's affected who she's become, whereas Gwen was sheltered and protected by loving parents. Gwen's death and Peter's transition to MJ is representative of his loss of innocence, and their mature adult relationship is one that can handle the weight and responsibility that comes with being Spider-Man. (Once again, OMD never happened in my eyes)
Honestly, that's why I was a little taken aback by the Woodley casting. I don't know what Webb was planning on doing with the character, but she comes across as being more youthful and more demure than Stone, when it should be the other way around. But maybe she can pull it off.
And I agree that MJ should have just as many (if not more) redeeming qualities than Gwen (the girl Peter should have ended up with) to balance the weight of Gwen's death. It's how the transition from 1st love to iconic love worked in Smallville. More importantly, it's how the transition worked in the original comics. I'm not a fan of the tomboy rebel/girl next door route either.