@ Cynder The Bloody Angel
...wait a second, WHO said Reshiram and Zekrom don't like each other? For all we know they may only exist in the universe of their respective games (as in Zekrom is never mentioned or alluded to in Pokemon Black, and vice versa) Dialga and Palkia aren't enemies. Neither are Ho-oh and Lugia.
Why on earth would you want the player to speak? NO VOICES. No one would agree on the "right" voice, and it would never work. I can guarantee you at least the main player won't be speaking. Besides that's way too much extra localization.
...and how on earth do you know already that in the games there is a fight to save the world? What if the evil team, or even just N's plans affect only Isshu? I mean yes, there are some things that are staples of Pokemon games, and there's no way around them. I mean would you want to just play through the games with no obstacles besides Gym Leaders? And what would any Pokemon location be without a source of crime? You're complaining about a staple part of Pokemon games... if you don't like it then quit whining and stop playing the games.
Yeah, multiple rivals are Cheren and Belle.
At this point everyone knows about the villains. But if this plot changing is available, events will eventually have to converge at some point: what could you possibly do if you were able to join Team Plasma and fulfill their goals? There wouldn't be much for you beyond that. So I doubt you'll be able to switch sides and go evil. But I hope there will be some changes depending on what you decide to do.