Although somewhat evened out in Battle Chess. The queen gets magic whilst the king... pulls out a bazooka from his robes. Among other standard comedy trope weaponry.
Commissar Ciaphas Cain's aide, Gunner Ferik Jurgen, probably qualifies somewhat. Cain himself isn't so much incompetent as merely lazy, fobbing off most of the boring office work onto his aide unless his personal involvement is absolutely necessary. Also the Battle Butler — Ciaphas is annoyed that none of the official histories mention Jurgen's part in his numerous victories.
"[Sememmnon] WAS the Black Network, having calmly picked up the pieces on innumerable occasions and ensured its smooth operation while his superiors raved, pursued mad schemes, or fought each other."
In Nomine fandom has Sparky; for actually running the Demon Domain of Technology while Vapula is....well...being a Mad Scientist.
Between Korg and Zet of Magi-Nation, Zet is by far the more intelligent and capable of the two, both in the animated series and in the game. However, for some reason Korg is Zet's superior; Korg's poor planning in both mediums results in much suffering for Zet. In the game at least, when Zet is finally alone, he not only proves to be smarter, but also much, much stronger.
Mutants & Masterminds: While the "Sidekick" feat buys you an NPC Cohort of less skill or ability, the game specifically suggests that you can play the character you build with this feat as your PC and the more able PC as your NPC Sidekick to duplicate instances of this occurring in comic books.
In Battletech's game storyline, heirs to the thrones of two Successor States around the time of the Clan Invasion, Victor Steiner-Davion and Hohiro Kurita, each have one that saves their butts several times: Galen Cox and Shin Yodama, respectively.
; for actually running the Demon Domain of Technology while Vapula is....well...being a Mad Scientist.