Well maybe Reshiram and Zekrom don't have to return, perhaps Kyurem has a substitution for them in both the movie and the third version, like the dragon gate and the god stone (the stone could have the essense of the other two dragons).
I've been thinking about Skyla's cargo plane and where in the third version she might take the player...an at first I thought Hoenn but then I remembered how Kanto always appears in each generation...and unless they make remakes of remakes there will be no kanto...
If they do Kanto we will be able to see what it looks like x number of years after HgSs...Also they could put either N or Ghetsis (or both) in kanto. The player could find Ghetsis by Mewtwo's cave (which could be empty and perhaps that's where Plasma put Genosect...). Also how cool would it be to be able to see Red and possibly Gold/Ethan (visiting kanto), Blue,Silver, Crystal/uh forgot her other name...,and maybe they could put green/leaf in the storyline for once.
Maybe N meets Red and sees the bond he has with his pokemon...