Doof at his core is a joke that can grow into something more. He can grow into being a competent supervillain or be a lovemuffin. A lovemuffin is not going to be a competitive king without an improbable amount of luck or gm fiat.
That's the thing, Doof is not a joke. Or if he is, he's a lethal joke. He's not capable
despite his various neuroses, he's capable because of his various neuroses. They're what allow him to pull off the frankly impossible shit he constantly does.
A Doof that can make a machine that shrinks the universe and isn't clueless about it is, what? Either he takes a huge nerf to ensure he can't just replicate one of his old inators or build new ones to that same power level, or he's automatically the most powerful King in existence.
So you cut out his wackiness, cut out his ability to do logic-defying stunts. You end up with a vaguely evil tech CEO who has mad science as a hobby, basically the same as every other Shadowrun megacorp owner. The purpose of inserting Doof into Shadowrun is not to drain all the Doofness out of him until only the Shadowrun is left.
None of those are true. Those are all extremely surface level traits, but look at the end of the TV Show where Doof retires from evil to teach in school, and at that scene in last day of summer where he's just enjoying muffins with Perry, Vanessa and Norm. Doofensmchirtz is not beyond character development, and has in fact already started down the same road, thanks to the help of some well-meaning employees.
Doof is not beyond character development, it's true. But his character development was him realizing that he didn't want to/have to be evil, not him realizing that he's too ineffective at evil and needs to be evil in a more socially-conforming way because he cannot possibly succeed at his objectives. His character development should be in the direction of being a happier person, not a more normal one.
Does this version of Doof even currently have a goal at all? And I mean, beyond beating various other Kings in the Shadowrun game, a goal for
himself? Sure, his previous goal was grandiose and crazy, but it was also something to shoot for. What would he even do with all his wealth and influence without an obssession to work towards, just let it sit there?