Actually, in some ways, the Brain didn't make such a bad choice, as all indications are that Eggplant Wizards are quite difficult enemies. Not only do they take a lot of hits before going down, but they can turn Pit into an eggplant that can move, but not attack. And in the show, he has the ability to do a lot of other magic involving vegetables. In fact, he's shown as being quite powerful, and might have proven to be an asset to the forces of evil if it weren't for the fact that he suffered from the typical cartoon henchman affliction of being stupid as all get-out.
There's still the question as to how the game designers came up with the idea of an Eggplant Wizard in the first place. Isn't Kid Icarus supposed to be at least loosely based on Greek mythology? According to Wikipedia, eggplants are native to India, and weren't known in Europe until the Middle Ages. Wouldn't a Cucumber Wizard have fit the theme better?
In one of the Captain N comics, there was a story about an island near Mount Olympus inhabited entirely by live fruits and vegetables, which could easily have been the origin of the Eggplant Wizards (and the one serving as Mother Brain's henchman has a significant role in the comic). Of course, there's no indication of this place in the actual game, but that's really the case for most of the Captain N comics. At least the show usually used actual characters and settings from the games, even if they never looked right. Anyway, most of the comics are available online, so I might have to review them at some point. One thing they DID do correctly was adding in Samus Aran as a character.