I think one of the main issues with the X-book now is the lingering Krakoa repercussions. Those that liked that era dislike that the X-Books don't emanate the same as they did during that time. Those that were 90s fans or earlier dislike that the current X-Books don't seem to resonate with what they remember either. Current editorial seems solely concerned with sales rather than cohesive storytelling, which amounts to "slap a #1 on it and shove it out the door." Krakoa seems to be a dividing line on a lot of things, villains included.
Of course that's not to say everyone feels like one or the other. I'm sure some have more nuanced views, but I and the majority of my X-fans in my circle seem to fall on one side or the other of that "Krakoa Era Complaint."
I think that's contributed to a "neutered" feel to some of the villains, as they did it earlier on with trying to stick Juggernaut in the X-Men. When he was back to being bad after that he never felt like quite the same threat. Sinister and Apocalypse should feel like off-the-wall long game threats when they appear. Magneto hasn't felt like an imposing or lethal threat to me since the Jim Lee X-Men #1 thru Fatal Attractions era. He came back somewhat with the New X-Men Xorn thing, and appeared to be becoming a threat again when he took over Genosha, but both of those seemed to get watered down before they switched gears into something else.