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For FRLG it has to be Koga. He gave me so much trouble it wasn't even funny! ;;
And for RSE it's the darling Brawly. Oh did he keep me from advancing so many times. On my first ever run through of Ruby I didn't defeat him until my team was mid-20's. \:
None of my favorites use my favourite type, however.
I like Blaine from FR/LG and Norman the best from R/S/E, though not neccessarily as opponents. I always thought that the trivia questions were fun in the Cinnabar Gym (even if they were easy), and I wish we would have gotten a little more backstory about Blaine and Mr. Fuji.
I liked that Norman was introduced as your father in R/S/E, and he is still the only one that we know of throughout all the games.
Winona is one of my all-time favorite gym leaders. Why? She's a freaking beast with her flying/dragon types! Tate & Liza comes in 2nd because the double gym battle was flipping awesome, and Wattson comes in 3rd because he makes me laugh :]
Wattson is so annoying. His gym is more steel than electric in Sapphire. The starter that you would think would have an advantage actually has it the hardest. Torchic is super effective against steel and mudkips ground typing negates electric attacks. Even with treekos resistance to electric none of his attacks do hardly any damage
EDIT: Oh my god I thought this was the most annoying gym leader thread, woops. Guess my vote stays with Wattson then but in reality I would have gone for Brawly, he pretty cool. O.O