Ugh, I hated how convoluted X Men The Last Stand was...it tried to do way too much within the constraints of one film and tie together storylines that didnt even cross over that well.
I think the thing the X-Men film universe has lacked IS that strong, young, female character. What I think people are wishing for is for that character to be there - what they did with Rogue was interesting, but it meant that that character didnt have a place in the films which is what we were expecting from her.
To be honest, aside from Mystique all of the main females in the X-Men films have been quite...wimpy? Storm's had her moments but she's never seemed *that* independent and always seemed to play a bit of second fiddle to Logan and the other characters.
The characters of the comics and the TV shows weren't to me given as much of a chance to shine or be as cool as they could have been, in the films. Of the women my favourite would be Mystique probably because at least she was quite badass, and I think that's what we were expecting of Rogue. Or at least for her to have been a complex character rather than just damaged. As I mentioned before I really like how they portray her in Ultimate.
Mystique came off brilliantly in the films, even without her original trademark costume.
Storm should've at least had a superior opponent in The Last Stand, in the final battle. Angela Bassett should've played her. She was made for that role. Whatserface was too petite.
The trouble with converting the original Rogue into the film was her immense power as a mutant. i.e. super strength/power of flight plus the absorption power, she would've had the film wrapped up in 10 minutes. I remember a couple of scraps in her early comic appearances would have her knocked out of battle initially, so other characters could have their 5 minutes of 'thunder', only for her to come round and bring the fight to a close! Either that or absorbing someones past which would disable her mentally.