It's strange, I don't know why but the battle with Red is so awesome, the music, especially with the old gameboy sounds is perfect. Pokemon needs more stuff like that in the main story.
QFT
I hope they don't ditch this idea, but don't just mimic it. In fact, I can see a good follow up in Black and White. Instead of just Red, its a series of all the games protagonists. I'd assume they would just choose a random gender for the ones that could be either way. If they did that, then I'd like to see at least one, like Ethan (name?), if May went on to be a big contender or some other guy, and he is looking for her, as she is training. Could be better, but I think the message is shared.
Also, they really need to go all out and make a "Battle Zone" or something that actually gets really tough. I'm sick of no wild pokemon being over level 60, and not being legendary. I mean, do they just naturally stop? I want a zone where your wading through pokemon in their upper limits of power, and you actually get real battles, instead of the quick experience juicy jokes that Mt. Silver provided. That would be Red shows up again. This time he has level 90+ pokemon. Just my hope anyways.