Another matchup idea I would love to see:
Oddly enough, after thinking it over, I would peg Doofenshmirtz to win hands-down. True, Drakken is a moderately more competent bad guy and more of a legitimate threat (as in, he’s never been beaten by a potted plant), but Doof actually has quite a few advantages over him in a one-on-one battle (per hypothesis, I’m excluding Shego from Drakken’s arsenal and Norm from Doof’s).
First of all, though he certainly can make his own, Drakken ends up stealing almost all of his doomsday devices, while Doof invents and builds all of his himself, which means that Doofenshmirtz is actually the superior evil scientist and would have more of a ready arsenal to draw upon. He once built a reverse ray for one of his own devices during a plane trip using nothing but parts of the plane itself; Drakken’s never shown anything like that level of ingenuity that I can recall. And while most of his inators aren’t obviously useful, he’s pretty good at applying them in creative ways when push comes to shove (he once successfully held off Red Skull using a ‘waffle inator’). Similarly, Drakken usually avoids physical combat himself, letting Shego handle that side of things, while Doof regularly tussles with Perry the Platypus. Granted, he loses every time, but he’s at least able to hold his own, meaning he’s got much more one-on-one combat experience than Drakken. Plus, Drakken loses badly every time he tries to actually fight, while whenever Doof goes up against another bad guy, he usually wins decisively.
Most importantly, Doofenshmirtz is kind of indestructible. He’s survived atmospheric re-entry, being blown up by a huge firework, and being trapped in another dimension without any lasting damage. Drakken’s gotten his share of slapstick punishment, but nothing on that scale. There’s really nothing he could throw at Doof that Doof hasn’t seen before.
I picture Drakken coming along to coax Doofenshmirtz into a partnership, then tries to betray him once he’s gotten what he wants. Doof has none of it and a duel of the incompetent evil scientists begins. In the end, Drakken manages to get control of one of Doof’s more deadly inators… only for him to inadvertently hit the self-destruct button and send him flying directly into OWCA’s lap.