- They all look different.
So? SMB3 and SMW wouldn't have been any worse with the bosses being 7 stick figures that looked exactly alike.
I got really sick of seeing Bowser Jr's ugly mug, back in Super Mario Sunshine, and have never liked the monstrosity. Ever. Why does Nintendo keep using characters everybody hates??
I never saw Navi after Ocarina of Time. Everyone hated her. Oh, and what about the dog from Duck Hunt?
(although I'm just as lost as you are on Waluigi)
In Bowser Jr.'s case, it's probably due to the fact that it's easier to develop one character than it is seven. And he takes up a lot less screen time than seven koopa kids. Sure, there's not a whole lot of character development in the Super Mario games, but it does exist, especially since technology has advanced to a point in which more storytelling can occur.