I've got a bunch.
I feel that Lieutenant Surge probably has the most interesting backstory, being involved at one point in his life in a war and using his Pokémon, which inevitably leads to a boatload of fan speculation. And, of course, he was born in AmericaFUCK YEAH.
All things told, I love Sabrina. She's eccentric and unexpected, and I honestly felt there was a strong character arc transforming her, and owing this to her defeats at the hands of her challengers. I think it's also interesting the broad scope of character personae she's donned in the various media; she portrayed as a psychotic sadistic bitch, a reluctant and lonesome recluse, a kindhearted clergywoman, and even a freaking member of Team Rocket.
Flannery was a great character by default; this was specifically exploited in the anime, whereby she was filling in as a replacement for her elders, the true leaders of the gym. Of course, this leads to some hilarious pitfalls for the character. After gleaning newfound confidence, she tests her skills and her willpower against the series protagonist to a battle and, although she has the upper hand, she ultimately loses as a result of being overconfident and reckless. She's perky, hot-headed, and a lot of fun to watch.
Claire and Koga were also somewhat interesting, especially as a result of their ties to their relatives and to the Elite Four.
There's also Gary (for obvious reasons being the rival) and Giovanni. I think there was something incredibly insidious of having the Boss of Team Rocket be the one who claimed possession of the Viridian City gym and called the shots on so many various occasions, always thwarting the direction of the heroes.
And lastly, Blaine. I think his determination and strong will truly set him apart from the others after watching his home and gym set ablaze by the volcano. And, of course, the strange connection between him and the events that transpired in the Pokémon mansion and the creation of Mewtwo.
