What killed Cyclops? This ASSUMES that he indeed does die, and FOX is not pulling a fast one on us (which I doubt they are).
What killed him? X3. Plain and simple. Many factors were involved, and I'm sure Hugh/Halle, had something to do with it, but that's not why he's got SUCH a small part. A rushed production schedule has little to do with it, because he wouldn't have been available, period. In my mind there are four main factors:
First and foremost, this was Wolverine, Xavier and Magneto's franchise. All three of those characters were going to get quite a bit of screentime in X3. Add more screentime for Storm to the equation, and Cyclops was not going to be a huge role, regardless of whether or not he was available.
Second, James Marsden choosing to do SUPERMAN RETURNS and having an availability that did not correspond to the scenes X3's production team had laid out at all (you do not shoot a film AROUND a supporting character), regardless of what you believe, had a LOT to do with his minimal part (I.E, he was available when they needed to shoot Phoenix scenes, but not available when the final battle sequence was to be shot or for anything in between). That is why he is only in a chunk of the film, and not put into a coma so he can reappear at the end. His schedule conflicted with the shooting schedule, period.
Third, I'm sure Wolverine and Storm's screentime had something to do with it, but so did Magneto's, Beast's, Angel's, Pyro's, Colossus's, Rogue's, Iceman's, Mystique's, Juggernaut's, etc. The fact is, even before Marsden chose to do SUPERMAN RETURNS, this film was PACKED with characters, characters that would not be seen if Cyclops had a meatier role. His minor part allows for them to take the spotlight. The writers and the studio both knew that.
Fourth, the writers clearly had limitations. They had Cyclops for a certain amount of time, and had to fit him into a certain shooting schedule because of it. They were inheriting a character who was already written out of half of X2, so doing that really wasn't an option. The only real way to put any drama into Cyclops's role was to kill him off and use it for the Phoenix storyline. Their only other real writing choice was to have him go into a coma and not wake up, or wake up at the end of the film, having had pretty much no part in it.
Remember, they did manage to sneak in some more stuff with Wolverine, and the romantic aspect with Jean/Phoenix before he dies.