Gen 1: OMG Mr. Mime... Don't even get me started... In my opinion one of the worst ideas ever in the Pokemon World... It's gender-unsure (come on, females are still called "Mr" at least make them 100% male...) and just creepy in a way (yes I dislike clowns in general too).
Second, I always thought Jynx was kinda weird and creepy too, looks like your gross and chubby aunt you never like to kiss. But at least it's 100% female...
Gen 2: The first Pokemon that I dislike in this Gen has to be Azumarill. Period. Just looks like a painted Easter Egg with huge ears (and it took AAAGES to catch a Marill in Mt. Mortar; NOT worth it!). Facing one in battle makes me want to KO it immediately.
Second, eventhough I trained one in my first adventure in the G/S/C games, I never found Jumpluff to be that useful and appealing.
Third, Smeargle. Just... omg .__. He is a pain to catch and then his only move, Sketch, is quite a creative move but I only find this useful when you manage to have the luck to get the timing right to copy a great move.
Fourth, sorry to say but I never liked Dunsparce all that much too. Just not appealing and useful (no evolution) in battles AT ALL. Sure, he is kinda cute in Mystery Dungeon for the 3DS, but... Gen.2? Never Ever gonna and will train one...