I was thinking about this, and my answer is that it probably has something too do with the 90s. That's when we got a lot of the villians like Fabian Cortez and Trevor Fitzroy. My other answer is that the X-Universe might be suited too dark storyline. Let's look at some of the characters and the events, shall we?
#The Mutant Massacare- This was a widescale tragedy in the X-Universe, and from what I understand, their first major atrocity. It gave us the Maraurders and Mr. Sinister, both evil too the core, and irredeemable. Monsters.
#Fabian Cortez- Very evil and monstrous. Didn't he lead the Acolytes on a mission to slaughter an entire hospital?
#Cyber and Sabretooth- Definitely monsters, especially Sabretooth. Completely evil characters. Although I guess that Sabretooth might have sometimes been a clone.
# The Weapon X Concentration Camp storyline- Another really evil and vile act that touched the X-titles. Dark stuff.
# Donald Pierce- Another complete monster. Very evil, but his actions have all been against mutants.
#Cameron Hodge- Do we have to go here? The Inferno babies thing that he did was just awful, and another example of a complete horror in the X-Universe. And then what he did too poor old Candy Southern and Warlock and Karma. This guy is a monster.
# Trevor Fitzroy- Yeah, he was pretty bad as well, wasn't he?
# The Genosha Tragedy
#Magneto's, er sorry, I mean Xorn's turning New York into something close to a concentration camp.
I'm sure that there are more that I can't think of right now, but it's pretty evident that the X-Universe is full of complete monsters. I don't mind, I'm just wondering why. I read some of Ultimate X-Men here and there (The first few Mark Millar and Bendis issues.), but I read that the Blob ATE somebody, and that Magneto was/is a pure psychopath.
If I recall correctly about the Ultimate Universe: Pietro and Wanda had an incestuous relationship, Magneto broke Professor Xavier's neck, killing him and the Blob ate Janet Van Dyne. For that, Hank Pym bit off his head. There was a lot of stuff in between but I kind of lost interest.