None of these would have bothered me either way. I didn't care whether or not Magneto found out about Peter, and the "No, I betrayed them," line was better, anyway, than Kinberg's line.
I have a problem with Apocalypse due to the same problem with X3, and that was the script. In Apocalypse specifically, the writing treats the audience like we're idiots.
1) The WHOLE WORLD has officially accepted mutants? And the only outliers to this are illegal organizations like cage fighting? We can't even get certain places on Earth to accept women...but every place is a-ok with a blue guy teleporting around a mall? No.
2) Magneto killed more people than the main villain. But because we see the destruction porn at a distance, we're too stupid to know that those dots flying off the bridges families in cars who died because Erik was having a bad day. This ruined the character for me.
3) The characters reverted to their FC status. Charles being naive in FC made sense--no one knew how humans would react to mutants and he's had a sheltered upbringing. 50-year-old Xavier would know better. He's a telepath, for Christ's sake, with mutant children who have come from different upbringings. And Erik...God. Fassbender did his best, but it's like having Bruce Wayne lose his parents, become Batman, be Batman in movie 2, and then--for no reason at all--decide not to be Batman in movie 3, have a family who--once again--is murdered and then repeats the same story arc as before. Rinse and repeat?--so, so unoriginal.
Bottom line, Kinberg did a great job with DOFP. The reviews were excellent, the box office was almost as good as The Winter Soldier, and it was well received by most fans. But when he can't conjure up enough conflict, he attempts to artificially create it by killing off characters and thinking that complex = depth and death = drama.
Him having total control of Dark Phoenix is just terrifying. I really hope I'm wrong here.