The following contains spoilers for Spider-Man: Homecoming.
In the months leading up to the release of Spider-Man: Homecoming, a great deal of attention was given to the character that Zendaya was playing as there was some question as to who she really was. One rumor claimed that her character was actually that of Mary Jane Watson, Spider-Man's traditional love interest in the comics, and, while the character was clearly named Michelle in the film, at the end we discover that she likes to go by the nickname MJ. Marvel's head Kevin Feige has now clarified that while this is a reference to the classic character, Michelle is still an entirely different character from Mary Jane. According to Feige...
Well, we never even looked at it as a big reveal necessarily but more of just a fun homage to his past adventures and his past love. She's not Mary Jane Watson. She never was Mary Jane Watson. She was always this new high school character, Michelle, who we know there's an 'M' in Michelle and an 'M' in Mary. [laughs] So we're so clever and we thought, 'Wouldn't it be neat if her initials were MJ?
When the rumors started going around a few months back that claimed that Zendaya was playing Mary Jane, a lot of people, as to be expected, flipped out online and while, as it turns out, there was a shred of truth to the initial rumor, it was only a shred. The way Kevin Feige describes the relationship to IGN, the fact that Michelle goes by MJ should be viewed as more of an easter egg than a statement that Michelle is Mary Jane. She's just a character with similar initials and isn't that cute?
While this explanation likely won't satisfy everybody, as many fans will always want to see Mary Jane Watson and Peter Parker together, it has to be said that in pretty much every way imaginable, Michelle is not Mary Jane. The only thing the two have in common is the initials. Mary Jane was very much the "girl next door" sort of character, and Michelle is absolutely not that. Her character is much more sarcastic than we would every expect Mary Jane to be. While Spider-Man is traditionally a hero who likes to run his mouth while fighting, Michelle may ever have Spider-Man beat in the one-liner department.
So, if you were concerned that the MCU was going to make radical changes to Mary Jane Watson, you can relax. Mary Jane isn't in the movie at all, instead, we have Michelle, an entirely new character who just happens to have similar initials, as a shoutout to those Marvel fans who might have been expecting to see her.