These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Complete Monster: Post-retool issues introduced a number of them. An alternate universe version of Jean Grey who made Nate destroy Quito killing thousands, murdered a little kid, Mind Raped and killed an unknown number of her genetic sons (after having sex with them) and tried to destroy half of the world. Qabiri who destroys entire worlds. From the earlier period we have Holocaust who very definitely established himself as such in his home reality.
Also the Parental Incest part. Madelyne (or 'Maddy' as he generally refers to her) is the only friend he has in the whole world. When she goes bad, it hurts him big time, though Jean does reach out to him.
It doesn't help that a whole bunch of 616 universe heroes were villains in the Age of Apocalypse, and vice versa.