I think an issue with Apocalypse is that he was a cackling two-dimensional caricature of a villain when introduced in the eighties, all genocidal and over the top and not even remotely needing to be 'fleshed out' or have any deeper motivations since he was for punching, not talking to.
Now he's getting some complexity added, as somewhat befits a dude who's been around for millenia, is ridiculously powerful, and yet, inexplicably, we'd never heard of having any significance, historically, ever before. (Uh, he napped a lot? Lol.)
Magneto went through the exact same evolution, over decades, and even suffered a regression to 'mad terrorist twat' before being salvaged back to the more nuanced character he had transitioned to. (No doubt Apocalypse will have similar bumps in his journey, as some writer who doesn't like a 'gray' portrayal of him and wants a more cut and dried 'this is the bad-guy, full stop' Apocalypse of his childhood, gets their hands on the character and drags him back to genocidal warmonger territory.)
Now, I should note, just because he's 'complex' or 'nuanced' or somewhat less a two-dimensional and over-the-top genocidal Darwinist maniac as he was when he woke up all cranky a few decades back, doesn't mean that I think he's morally right about anything.
(Honestly, I wake up after a 1000 year nap and have no coffee, I'll probably want to kill a few million peeps too...)
I'm still not convinced that Magneto is right about anything. He's just more enjoyable to read about now. Ditto Emma, for that matter. Her methods and motives can be self-serving and sketchy and undemocratically aristocratically elitist as hell, but she's *fun* to read about.
I can enjoy their antics without necessarily thinking they are all 'good people' or admirable role-models or pillars of moral (or ethical) rectitude.