The Dark Phoenix is easily [one of the worst threats to burden the Marvel Universe](https://marvel.fandom.com/wiki/JeanGrey(Earth-616), bearing incomparable power and, unfortunately, a healthy side helping of evil too.
Her only real weakness is that, despite her godly presence, Jean Grey’s body is still mortal, meaning that if Wonder Woman can manage one devastating blow, that would be enough to stop her, but it would still be a hard road to travel.
You could name any Marvel villain and pick an ability of theirs at random, and she probably has it, in addition to molecular reconstruction of all matter and the ability to generate energy blasts strong enough to destroy whole planets.