First, killing off Cyclops was a terrible decision. He could have been in X3, but Fox didn't want Mardsen back and wanted to punish him for doing SR. Look what else came that summer, Ian McKellan managed to be in X3 and The DaVinci Code because X3 was shot so late, most filming for the other pictures had finished. They could have accomdated Mardsen like McKellan but chose not to, so we get the character killed off. Fox also wanted Wolverine (Hugh Jackman) more center and wanted to write out "the other man," even though technically Logan was the other man.
Curing off Rogue was a terrible decision that all agreed upon. It should NEVER have been an option. As for Mystique. That was just shoddy writing. If they wanted to write her character out of the movie, fine. But they could have done it in a moving way. Have her cured and Magneto try to care for her, but she is extremely sad and Magneto kills her and uses her death to galvanize her supporters, etc. The relationship Singer built up between the two in X2 was a great one and for him to walk away from her in the same breath he says "You saved me!" was ridiculous. It was shoddy writing and unemotional because it rang out of character and hollow. Just as that whole scene where all the "bad mutants" join Magneto without asking questions or having any personalities or motivations of their own. They were there for SFX and the movie was blunt about as the writers didn't even try to explain them. Nor did they explain Magneto's actions well because it was out of character...like Wolverine becoming a team leader, Xavier talking like an ******* to his proteges, Rogue deciding to cure herself, etc.