Yeah it seems like a golden opportunity to me, especially because we've been told that one of the themes in this movie is going to be about second chances. Xavier IMO bears a lot of responsibility for what happened to Jean -- she didn't even have the Phoenix personality until after he started to tinker around in her brain. I've never liked his attitude in X3: he was way too arrogant (and yes, I know that in the 616 he has been presented that way at times: but I don't really like it there either).Same I'll be disappointed if he doesn't. Like all fans I want to see Jean and Cyke return at the end when Logan awakens. Telling him to stop Scott going to Alkali lake or not suppressing Jeans powers would save them.
Fox knows he much fans want that. I'm a fox supporter as I have liked the majority of X-Men movies but ignoring that would make me quite mad at them.
Did it answer questions, absolutely! The Yashida thing just doesn't make sense to me. If we're going to take in every films marketing into canon, while we're at it, remember the search engine on the X3 official site. You could search Bolivar Trask which gave you his bio, you could search Sentinels and Project Wide-awake which came up classified. You could also search strange occurrences near Alkali Lake which mentioned strange lights hinting at Phoenix and yet none of these things count anymore. So how far can we really take these things?