I dunno, I think Bidoof is adorable, actually. And the one in Mystery Dungeon's a pretty cool guy. Bibarel... okay, kinda weird-looking, but it's supposed to be a goofy-looking beaver. (I think it's the eyes, mostly. They stare into your soooouuuuulll)
Frankly, I believe that a lot of it is due to nostalgia-induced Gen IV hate. Plain and simple. They're no less unoriginal or ugly than other Pokemon. (I mean, seriously, people uphold first-gen as this standard of brilliance, but remember Voltorb? "Hey, when it evolves... let's flip its colors upside-down! BRILLIANT!")