Going into Apocalypse, I had no problem with Magneto and Mystique being in this. I mean, they're going up against one of the biggest villains in X-Men history so it made sense. Now that I've seen the movie though, I would have to agree - I wouldn't have had either of them in it if this is what we got from them, but they weren't going to drop Fassbender and Lawrence which is completely understandable. They just needed to write better roles for them.
I think the film would have worked better had they have made Professor X, Magneto, Mystique + one other character the horsemen from the beginning and not by their own choice - kind of like what they did in X-Men: Evolution. That way, it would have been a great opportunity to really shine the light on the younger team and have them work together to save the older generation.