I know it is going to sound crazy but I just watched the new episodes of Ultimate Spiderman so major spoilers here anyway I saw her as Carnage Queen (like the idea but would prefer her to just be Carnage) anyway how would you feel if they made her the new Carnage? I can see her life slowly falling apart because of Peters secret life as Spiderman and for her to slowly grow resentful and then find out she's of all things pregnant. Essentially I'd like Carnage (who might finally decide to just kill Spiderman once and for all) to kidnap Mary Jane and torture her for a while and then ultimately she miscarries and in state an emotional break down blames the situation on Peter (he was the original symbiote host and well a lot can probably be traced back to him).
Not long after the final show down with Cetus takes place at the church Eddie became Venom(I love symbolism and poetic twists and turns) and the fight kicks off with Cletus dropping a severely traumatized MJ off a high ledge (spiderman saves her leaves her tied up in a web suspended inside the church (you probably see where I'm going with this) the fight with Cletus Cassidy reaches its climax and Spiderman separates the symbiote but goes further and is so angry over what Cletus Cassidy has done he either beats him to death or just lets(and watches) him die separated from Carnage all while a storm(I think in most versions there was a storm when Eddie became Venom) is starting up and the symbiote dissapears and Peter is too busy beating on Cassidy/watching him die to care.
In the end Cletus Cassidy dies Peter goes to get MJ but to his horror discovers that she's been taken over by the newly free symbiote and has become bat-shit crazy saying "There is no Mary Jane only Carnage!" I honestly would love for this to happen because Peter having to face the woman he loves as one of his enemies would be a good plot especially if MJ as Carnage professed love for him while trying to kill him. As for the kind of villain she could be I can see her putting Peter in situations where he's emotionally tormented and has to make a terrible decision like she rigs a bomb or something to a hostage or group and the only way to disarm it is to kill her or she sets up a situation where Peter can only save one person.
Not going to lie the more I think about it MJ might potentially be Peter's most dangerous enemy. I mean she probably knows things and has an insight into him that nobody not even the Venom Symbiote/ Eddie Brock knows or has. I mean really she could hurt him in ways that no one else could.
I really would love something like that to happen.