I think a lot of people thought it would be like Duckman; which was Everett Peck's (creator of Squirrel Boy) first show. I've never seen Duckman, but I do know it's a lot older, and geared towards more mature audiences. Squirrel Boy is intended for younger audiences by comparison, so I'm guessing all the Duckman fans were disappointed.
Maybe Squirrel Boy wasn't hated, but it was definitely under-appreciated.
I think a lot of people thought it would be like Duckman; which was Everett Peck's (creator of Squir