One of those is the Grail novel. Jean, using her enhanced powers and knowledge of medicine is able to fix Scott's brain damage so that he is indeed able to control his powers, at least to turn them on and off. You're probably thinking he'd have to give up his visor, but no. He can turn his beams on and off, but his shots are clumsy and awkward. Jean helps him realize that the visor can still serve a useful purpose, as it allows him to modulate and set the power output of his beams in a way that he could never do naturally. So on a normal day, he's not Scott "blue-eyed" Summers, but on a mission, he's styll the Cyclops everyone knows. Except now, you can't make him blind by knocking the visor off his face
Oh indeed. It's a shame movie companies can't swallow their pride and let them adopt one of their stories into an actual movie. It'd be far superior and far more engaging IMHO to anything those paid-by-the-script hacks come up with.