Yes, the main characters in Fury of the Furries are conceptually flawed to a degree, within the framework of most schools of thought on how to design main characters.
Even Kirby had unique features. He grew 4x his size when he puffed in air, for one, and his ability to absorb enemy features helped (it changed his appearance in later games), and his design was originally just a placeholder sprite.
Kirby has memorable animations and abilities. This is key, any single frame of a Kirby sprite is pretty much a pink blob doing gay (happy! I mean happy!) things. Yet in motion he's pretty memorable. This is a good lesson to learn for your main character, PypeBros: animate cleanly, extensively, with character and purpose, all the various abilities of your ball sprite mainman. Now, I won't lie to you, ball main characters are the absolute staple of 'hello, I am a programmer making a game for the first time!' types of games. They evolved directly from programmer placeholder art, and they're not a very good idea for a game character outside that context, Rayman legs and arms notwithstanding. I'd go as far as to say that any other platonic solid would be more interesting to look at than a ball. Give me a triangle or a square or a polyhedron rolling around with little Rayman arms and legs and expressions, I'll be slightly, just slightly more endeared to them.
All that being said, the 'hello I am a ball' main character didn't stop 'Within A Deep Forest' by the Knytt dude from being a good game, but were he to come to Pixelation and ask for critique for his game, he'd rightly be said that a ball is no good main character, no matter how good the gameplay mechanics came out to be.