I think the thing I like most about Professor Venomous is that he's so far removed from other cartoon villains, including Boxman. He rarely acts like or resembles any villain stereotypes--he's just a severely messed-up dude, and it's his own fault from poorly managing his insecurities (I wish we could've learned more about his past before P.O.I.N.T.).
Despite this, he still has traits (even positive ones) that make him seem pretty chill and down-to-earth. He could be a cool guy if he didn't have such a severe inferiority complex and light sadistic tendencies.
He cares about Fink like a daughter, and according to Ian J.Q., he genuinely wanted to know and get along with K.O. He just never learned how to actually be a father, and has no sense of discipline, even for himself.
On a side note, the show is transparent about the fact that two unmarried characters had unprotected sex (the only reason K.O. exists), which was previously unheard of in cartoons aimed at kids/teens until about the past 15 years or so. The show also addressed absentee father issues in a way kids could understand.
Getting back to Venomous, another surprising thing is that he falls in love with the highly ineffectual lesser villain in the series. Boxman is the antithesis of Venomous--being an amalgamation of cliché and obnoxious cartoon villain stereotypes--yet he has Venomous completely enamored, almost to a fault (it takes laughably little for Venomous to forgive him for even the most monumental screw-ups).
Boxman does manage to break free of some of his stereotypes, and it's because of Venomous. Aside from later interference from Shadowy Figure, the romantic relationship between the two is shown to be surprisingly healthy, and built on a foundation of mutual support.
It's nice to see the goofy villain end up with their crush, and the "attractive" one falling for someone you might not expect them to.