For me it's Salamence--a very popular, very good Pokemon but god do I hate how it looks. It looks like a long-necked alligator with construction-paper wings stuck on it. It looks slow, not fast, and not at all able to fly. It's pretty much the only Dragon type in the game that squats on all fours with stubby legs (at least the only fully-evolved one, IIRC).
So what's your Pokemon that you just hate the design of, even if you know it's good or use it yourself?
"It's hard to reason people out of positions they didn't reason themselves into." --JonWood