I understand how important comic book continuity is, but it's clear in most cases that it should be only used as a backdrop and for story purposes, but it shouldn't be followed exactly if it'll inhibit the story. You need to sometimes modify, change names, and move times around in order to make the best movie possible. Like I said before, Batman Begins and TDK were the perfect examples of using the basic source material, but changing aspects around a bit to make the best movie possible.
One of the disadvantages of the X-Men franchises originates entirely upon the struggles from making the very first film. I have 100% confidence that IF X-Men was given the appropriate funding and time that Bryan Singer hoped for, that we would've gotten, not necessarily a better movie, but a movie with more attributed from the comics, not necessarily in terms of accuracy, but of a quantitative measure. Since the following sequels had to draw everything from that, it was definitely an influential aspect into all that followed.
as for accountability on X3's part, I'm sure there's more than enough blame to put on just one person. In my eyes, it was a combination of decision making from the actors. Bryan Singer, Matthew Vaughn, Zak Penn, Simon Kinberg, Studio producers, Brett Ratner, and maybe even more. There were so many hands put into X3's production, you could take your pick for whatever you liked or didn't like about the movie. Honestly, the movie is actually quite good, but it just failed to meet such high expectations. It also makes you realize how special and important X1 and particularly X2 really were, despite people's opinions about them now.
-TNC