...there are so many alternate timelines, etc. J2 is actually questionable because he's from the MC2 universe, not the mainstream Marvel timeline.

Off the top of my head, there's a few:

Polaris, Scarlet Witch, and Quicksilver (Magneto)

Toxin (well, sort of) (Venom, Carnage)

Alicia Masters (Not a hero, but her father IS the Puppet Master)

Hulkling (His father was Captain Mar-vell and his mother was a Skrull Princess. Technically, she wasn't a villain, but in light of recent events, I'm more likely to paint all Skrulls as villains...)

The Runaways (probably the MOST obvious since it was the entire plot of their first run. You've got the Pride, and one of them has Ultron for a father!)

Awesome Andy (This is a bit of a stretch, but he was created by the Mad Thinker...)