She walked away awkwardly in the end. She might come back.
Another waste was Jubilee, very well-portrayed, but just a meaningless cameo.
But, in hindsight, the one crucial mistake with this film was Jean Grey's development. Jean Grey pops out of nowhere with the Phoenix Force. And they should have built up to that. Maybe have Jean Grey meditating and training in the astral plane throughout the film to take down Apocalypse in the end. See, when Apocalypse hacked Cerebro, Professor X could have counterattacked by engaging Apocalypse in his mind then, not at the end of the film, but in the middle. After Charles' abduction, Jean could realize that that may be only the way to stop him and sets out to do so. Explaining the restraints which Charles applied to her powers would have also made sense, given she needs to break past them to unleash that power.
I feel that walk on air would have been a lot more compelling with a bit more development. Especially for an origins story of sorts. You can't just expect audiences to know what the heck's going on.