I'd really have to agree with this. Throughout the entire game (in both Johto and Kanto), you hear about the trainer from three years ago that took down Team Rocket. You hear from his old rival how he was beat by him and lost his championship title to him. You even hear about the little things like giving the Mimic Girl in Saffron City a Poke Doll. He's built up as this legendary trainer, but you don't think you'll ever cross paths with him because, well... he was the player character of the first gen, and a silent protagonist at that. How would that even work, right? Then you get sent to Mt. Silver without much fanfare, and suddenly, the guy you probably spent a good amount of time playing as in the original games is now the true final boss of the newest entry.
Another one of my favorites is Genya "I'm totally not Alucard" Arikado from the Castlevania Sorrow duo:
Pretty great use of the character, in my opinion.