To much mystique? in marketing maybe, but really there wasn't too much mystique in the movie at all, infact lawrence may have been pretty bored in the role since there was very little for her to do, no action this time, no attempt at making her complex or anything, she was basically just playing the same character as in DOFP but without the action and darker side.
As for Xavier and Magneto... the only repetitive side to it was Xavier once again trying to talk magneto out of doing something bad, other then that they didn't have that many scenes together anyway and honestly after the way apocalypse ended i can see them turning magneto into more an anti-hero.
Overall i don't think those characters were the issue with Apocalypse, more so it probably had the same issue as Superman returns, it felt more like singers personal love letter to the last 2 movies and the OT.
I get that some people want other X-Men to be upfront now but honestly the issue with apocalypse was not xavier,magneto and mystique, it was more the execution which was played on too safe while also trying to be abit of everything.