My view on the Cyclops thing is this: He got the short end of the stick through the whole trilogy and being killed off was a crappy send-off, but it wasn't the original plan - it's just the option that Bryan Singer and James Marsden's departures left. The reason Rogue is AWOL throughout the entire movie and why Mystique is cured in her third scene is because the movie was made so quickly that not all of the actors could commit to the full shoot schedule, so we got what we got. But with that in mind, I do think that Scott got a send-off that did his character justice. He died for the woman he loved, which is what he was willing to do in X2, so he at least died knowing that he hadn't completely failed Jean by not being able to save her - he did probably realize that perhaps he had bad taste in women by that point, though.
Originally Posted by ALittlePush
In X3, Rogue says to Wolverine “I want to be able to touch people. A hug, a handshake, a kiss.” Yet in X2 and the alternate X3 ending, she hugs Bobby quite happily with her powers. Therefore her powers don’t stop her from hugging anyone so long as she doesn’t touch their skin.
I take the Rogue scene as her stating that things Logan may take for granted are things she has to consider everyday. She needed to be covered up at all times just so nobody accidentally gets hurt because of her. So the hug line maybe wasn't a literal concern of hers, but it sounded much better than her saying to her father figure in the movie "I just wanna kiss and screw mah boyfriend!!!" - it was a much more poetic way to state her problems.