Pokémon Gray. I've heard Chrome as a suggestion, but knowing Nintendo, they'd keep it simple and sweet for the kiddies.
Again, Nintendo wants to keep it simple, so it'll likely be Kyurem. However, if anyone's noticed how parts of it seem to be missing/broken, I speculate they may give Kyurem an alternate forme like with Giratina or a completed look made just for this game.
Well, if I recall correctly, Nintendo seemed to put both version-exclusives in Emerald but took them all out in Platinum (excluding the Dragons), so they might do one or the other with the third game. As for Drayden versus Iris, they might choose who you will fight based on your gender. And Opelucid will also look like/have the same music based on who the gym leader is (in other words, a city with techno music for Drayden and a ruin-esce town with folk-ish music). Mistralton would be a mix of fields and buildings by the runway.
Regarding Black City and White Forest, why not make a town specifically for the third game? If not, it can be like in Platinum with the two fossils: It all depends on your Trainer ID. If it's odd, it'll be one place. If it's even, it'll be the other. The same could also go for the eighth gym leader.
Finally, Triple/Rotation Battles. I'm guessing they may alternate. Like in the house in Opelucid one floor could be for Triple Battles while the other would be for Rotation Battles. However, if they want it to be an even number, they'd have to add at least one more trainer since there are seven trainers who do Triple/Rotation Battles in-game.
I can honestly see N gaining control of both Reshiram and Zekrom at Dragonspiral Tower, causing Kyurem to go all mad. However, they would be at lower levels than Kyurem rather than at higher levels, just to give Kyurem a chance. I can also see N releasing both and flying off on Archeops rather than the Dragon. Or, as mentioned before, the Dragon he gets is based on one's gender or Trainer ID. However, one problem is that the Giant Chasm would either have to house another legendary (maybe one of the roaming kami trio? probably not though.) or, like with Spear Pillar in Plat., one could find both Reshiram and Zekrom. Maybe the game will even let you go as far to catch Kyurem, though I highly doubt it. I'm just not sure how they'd work that out.
I would also like to see the player getting the chance to fight the other six Sages upon meeting them after Ghetsis flees, and maybe even the Shadow Triad (though I doubt it).