I agree that they should have just stuck to the Phoenix story-line and had all the X-men teaming up, with Jean finally having to do the internal fighting, as she has done in all the Phoenix versions. The cartoon Phoenix Saga was better than X3 - and I actually do think these movies owe a certain obligation to staying true to the comics to an extent.
I myself preffered Superman Returns to the other Superman movies, I just thought that X3 would have been a lot better with Singer behind it. I thought the actress that played Louis Lane was terrible in 'SR' though - she wasn't strong enough - and her wig was terrible LOL. I'm also so bored with seeing Lex as the only villain. There are way more interesting ones which they havn't used. I think Smallville does a better job with Supes than anything else. I wish they'd cast Tom Welling instead of Brandon Routh (he's a much better Superman I think), who was obviously only cast because he looked so much like Christopher Reeves, who I never thought fitted the part of Supes anyways, although I liked his Clark Kent. Superman has always been too good for my liking, I always preffered Batman to the 'boy-scout' LOL.
I thought Rogue was dealt with okay in the movies...I mean if they'd done her full intro then you'd have the whole past with Mystique and her putting Ms Marvel in a coma, which I hated Rogue for. IMO, Rogue is a lot like Wolvrine in the way they've given her far too much power in the comics and not enough personality.
With comic book movies, I have to say the thing that has annoyed me more than anything, was to put MJ in Gwen Stacy's role in the first Spider-man. I was literally furious! I love Gwen, and that was one of the biggest comic stories of all time - you just don't change thing's like that. I do like the spider-man movies though, and I can't wait for 4 and 5.
I still havn't seen Watchmen, I've actually never got into the comics TBH, although my friend likes them a lot.