(Player pants after long run, or calmly walks out of a plane/train before hurriedly panting, shouting out at wherever he was dropped off, "...Kanto...in an iceage...it's coming for you." Townsfolk looks at the stranger mumbling about crazy tourists, before this one believer runs up, and says, "Hey, I believe you, my ____ called me about it. If you want anyone to listen to you though, you're going to have to get our 8 badges, it's a respect kind of thing.")
Not going to troll you with the rest of the dialogue, but you get the idea the game would be one of those "Confident about saving an entire region, Crap I forgot my mons even though we had a very strong bond, Bitter towards these new Pokemon until I get attached, and half of the region is frozen by the time we get to the league, with the survivors all gathered there to come up with a plan." If you're going for a funny game though Badhaas then by all means go for it(Just make sure you have a good mapper though).
Haha! I haven't played BW2 just yet, so it was purely a coincidence! Yeah it's a bit crap, but trying to fit in every region without an over-arching storyline is/would be tough. I mean, wanting to be "the very best" is all well and good, but the game might feel super-stale without something to drive you through. But in defence of leaving the Pokes behind, it's not that they are forgotten. More like, whatever the problem is leaves your Pokeballs busted and unable to function (kinda like what has happened on occasion in the Adventures manga). Bear in mind though that despite it sounding awful (as it does in hindsight), it's not as if it needs to be like high art or something. It's Pokemon. Campy "teams" and cute baby monsters shaped like adorbs animals. Depending on the choices made regarding levels and stuff, you just need a believable excuse to justify your choices that fit within the constructed universe.
Darkroman you make a very good point in your post, and I doubt I could put it any better. In fact when I read that I completely veto the idea of the team reset part-way through. After all if you can't fight against Roxanne with a (Mega!) Blastoise, then there really isn't much of a point.