Johto: Clair. I've always loved her and used to be like obsessed with her back when G/S/C first came out. Her character design has always been awesome, but it's even more awesome now. =D Not to mention, Dragon Pokemon have always been my favorites, so that's a major plus.
Kanto: Lt. Surge. I thought he was so hillarious in the anime. I loved that episode, and used to watch it over and over (taped it). And he mains with Raichu, which is one of my all-time favorite Pokemon. ;)