A lot of people have brought up the possibility of Hoenn, but straight RS remakes released six months after B2/W2 are far more likely. Why would a sequel to "a new world filled with never-before-seen Pokémon" take place anywhere other than Unova?
Of course, we don't even know if these are sequels or not. We could have our first ever international fourth version, or we could even have prequels.
If these are sequels, I'd look for a G/S/C feel to it. You'd start in a newly introduced part of Unova, and the plot would start tying into the plot of B/W around halfway through.
If these are the equivalent of a third version, I'd expect gym rematches, a Battle Frontier, and the rest of the usual third version stuff. We've all figured out by now that N would get Reshiram and Zekrom, the player has to catch Kyurem, yadda yadda yadda.
In the extremely unlikely event we get our first prequels in series history, we'd get to see N's backstory and (probably) the identity of his real parents. That would be better left to fanon.
Regardless of what B2/W2 actually are, I'd also expect Keldeo and Meloetta to be event-catchable (similar to Deoxys in FR/LG/Emerald) now that they're revealed. Possibly Genesect as well.
As for the identities of the Shadow Triad... I'm predicting that they are NOT the Striaton trio, since that would massively derail the anime, which hasn't even introduced Team Plasma yet.
If the ST does not exist in the anime, and only in the games and the various manga, I could see this working out, though. Adventures/Special dropped a pretty huge hint that the rumor is true in that canon.
Finally, Mewtwo will be catchable despite the current Wi-Fi event's existence, UNLESS there are another set of R/B remakes which I can't really see happening until 2014 in Japan. Speaking of which... happy birthday, Pokémon. 16 years since Red and Green...