TVman: Simple.
First you have a catch all boss. A boss that will be used for any character series that doesn't really fit the mold of having a special final boss. These characters would include: 3rd party characters, Wario, Mr. Game and Watch, Ice Climbers, ect.
Think you create final bosses for series, not individual characters.
Mario Brothers Characters can face a boss from the Super Mario RPG series.
Samus Mother Brain
The Zelda Characters Vaati
Basically, I would see the game having a total of 5-6 different bosses period. Not a big difference, but enough for replay value.