1) Riku. The only character to actually change through the games. Did what he thought was right(and also what got the job done), even though many didn't approve of it. While Sora and the crew were out screwing around he actually found kairi(and in the second game he was waging a "secret-war" against the ORG while sora was,again, screwing around.) Even though he originally fought for the darkness, he excepted both(light and darkness), without being corrupted by one or the other.
2)Zexion. The scholar who frankly, I believe, knew the most in all the games. He, while the rest of the organization was fighting within itself, was planning strategies, studying, and semi-leading the organization from the background.He also was one of the few people who wasn't under xemnas's control.