Hmm, it depends.
Throwing out all the silly games past Red/Blue(Green), there's no doubt that psychic pokemon were the best, and
Alakazam and Mewtwo were the best of them. Yeah, you could gameplan around how to beat psychic pokemon, but the fact that only a handful of pokemon were effective against them and other trainers were practically forced to carry them showed how dominant they were.
Now, in terms of overall favorites, I gotta go with
Articuno. Loved that bird
