Well, I like a lot of pokemon, I don't think I really hate any but have a large dislike for some.
Kanto:
Magikarp.
Zubat.
Jynx.. I never knew if it was a man or woman. Especially by the voices from the anime. Scarred me for life.
Pidgey and Rattata for being on too many of the starter routes.
Metapod and Kakuna for being useless when you catch them and only knowing Harden, yet when Bug trainers have them, they know tackle and other moves.
And of course, most of the Safari Zone pokemon because they were so difficult to catch. But, I think that execute annoyed most since it always popped up when I played.
Then of course, the pokemon at celadon's prize place annoyed me since they cost way too many points. Especially Porygon.. then once you get it you think it'll be awesome and you find out it really wasn't too awesome.
Johto:
Miltank
Hoothoot, it was nearly on every beginning route and I always ran into it, yelling loudly in the process.
Red Gyarados. Again, you think it's made of awesome and it's hard to catch, so you think you're getting something great, but then you get just a plain Gyarados that's red.
Sudowoodo since it's a tree. A tree! I couldn't believe they made a tree pokemon.
The baby pokemon, because it was annoying to breed just to get them.
all the Unknown pokemon because I could never find every letter. I had like 3 missing and they never showed up.