In my mind Gray will be a sequel of Black/White. The reason I say that is because the last thing relevant to the story said in the game is something along the lines of "A boy with green hair was spotted flying on a Black/White Dragon. I have to go. If I see you again we will talk more". It's begging for a sequel.
We all know there won't be another pokemon game for the DS, so I think that Gamefreak will just make G VI for the 3DS with Grey to kick it off.
What I hope for is that you start out as the character from Black/White with some good lvl 60-70 pokemon (Zekrom/Reshiram being one of them). After the tutorial as the character from Black/White and the possible start of another war you switch to a newbie trainer.
What I want in Gray
-Shadow Pokemon (Like the gamecube games)
-Multiple Regons accessed by Boat, Train or Plane (like being able to visit Orre, Hoen and Sinoh or something)
-History based storyline (Getting to know more about Pokearth and the legendary lore)
-Mentions of past 'Heroes'
On the topic of Kyurem, I do think he is the shell of some type of Legendary or God. Maybe he was too powerful so they scooped out his insides, soul or power and turned them/it into the Godstone, that would explain his mangled appearance and use of the Ice element. But that is a bit dark for Pokemon.
I think we would be better story writers than the people at Gamefreak. Heh.