Alternative Character Interpretation: In-universe, as a running theme of the book is that the heroes and villains, despite defining each other's lives and fighting each other for years, really don't know or understand each other at all.
Doctor Impossible receives a very sympathetic portrayal as a sufferer of Malign Hyper-Cognition Disorder which shows him to be insane rather than evil. However, we encounter a superhero who Doctor Impossible says is almost as smart as him but not evil (which makes him "kind of stupid" in the Doctor's view). This is a blink and you'll miss it moment but calls into serious question whether Malign Hyper-Cognition Disorder even exists. The only other time MHCD is mentioned is to Fatale by Damsel, who gives her a wink indicating she thinks the whole thing is one gigantic joke. It may be that Doctor Impossible is not insane in any way at all, he's just evil.
It's also possible that Doctor Impossible has a mental disorder entirely unrelated to his intelligence. Even if MCHD is false, he likely has some sort of compulsive disorder.
Is Corefire a Fantastic Racism Jerk Sue? Doctor Impossible says he's a Good Is Dumb type but Corefire is one of the few scientists able to keep up with him. Lilly and he both think he's something of an arrogant Jerk Jock type regardless while Fatale's impression is he's actually kind of shy and just overworked. Damsel says he dumped her because she's an alien but given she's publicly the daughter of an alien princess, is it possible there's another reason? Like the fact she's actually an Opposite-Sex Clone? In which case the racism is more gendered. Or possibly CoreFire realized there was something creepy about having sex with the daughter of his hero and role model?
CoreFire is labelled as insensitive and oblivious to others but after what has to be the most humiliating experience of his life he takes the time to show a total stranger, Fatale, where to find information about herself in Impossible's computer.
The Woobie: Doctor Impossible is this given he's constantly beaten up, abused, and knocked around by heroes. The fact he deserves it for trying to take over the world is undermined by the fact he's mentally ill and can't help himself. Albeit, see Alternative Character Interpretation.