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.
Is Corefire a Fantastic RacismJerkass 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.
Foe Yay: Like any decent supervillain, Doctor Impossible just can't stop obsessing over his nemesis Corefire.
Fridge Logic: Why did Doctor Impossible try to hide his identity with a napkin in the big fight with the New Champions? He didn't have a mask in prison, he's probably been scanned down to the subatomic level, and the Feds would clearly have a photograph of him without his costume. Heck, even a couple in the diner recognized him.
Well, part of his Internal Monologue is about how he sometimes couldn't help himself: building Domesday machines, spouting one-liners; heck he had trouble preventing himself from explaining his plan at one point. Maybe wearing a disguise when fighting heroes was one of those things he felt was necessary... or he just couldn't help himself.
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 Alternate Character Interpretation.