well you have said to others what i have been trying to say for years.wolverine was most popular x-men character for years before the films.why do people think singer and donner wanted him to be focal character in first place.and marvel itself overextended his use in comics.ask people in 80's and 90's if there was ever going to be x-men films and they wouldn't use wolverine they would have thought you were crazy.
Indeed! The problem is that most of these "comic-book accuracy arguments" are not based on any logic but on a very specific head canons of some fan individuals who claim ownership over these characters. In the end, you can always find the right comic book storyline to justify the movie-verse handing of these characters. Wolverine was and is the most beloved X-Men. I don't particular care about him but obviously (and sadly) he has a great masculine, mainstream pull. the marvel universe also rotates around white, cocky males (Thor, Captain America, Ant-Man, Spider-Man, Iron Man are basically the same archetypical character). It is the sad reality of mainstream cinema coming from the United States...
I personally love what they have done with Magneto, Xavier, Wolverine, Mystique, and Jean Grey so far. They decided to give these handful of characters some wonderful depths and development. Following the life stories of these characters through so many time periods have been nothing but pleasant!
And now the new trilogy will start and they will obviously shift the focus to a new team introduced in "X:Apocalypse". So anybody should be happy. Luckily, they will not abandon characters like Xavier, Magneto and Mystique altogether!