Kanto: Major Bob, definitely.
Johto: Whitney, with her stupid Miltank
Hoenn: Norman really gave me hell the first time around, and remained a challenge in latter playthroughs.
Sinnoh: Fantina. I just hate Ghost types.
Unova: Drayden. In Gen 5, dragons were still OP, remember?
Kalos: Valerie. I just can't wrap my head around the weaknesses of Fairy Pokémon.