I agree with Dusty Dog. I think it'll probably be Mt. Silver, if not, then where else?
Mt. Silver is an unlikely place for Kyogre and Groudon to be situated in as it is said to [probably] be the place holder for the Arceus event where the level one Palkia, Dialga, and Giratina are unlocked. So, my mind really doesn't go to the heights of Mt. Silver, but more or less to a fixed location like most have been thinking. Seeing as they are both version exclusive, and their surrounding areas from the scans seem to look similar I would think they would be located in one area, rather than two difference places. If it were to be one fixed location though, I wouldn't be surprised to it be a new area made within the game. As for Rayquaza however, the Dragon's Den does seem probabale, so we'll see.
I think maybe you have a side quest to Hoenn only to go where Kyogre/Groudon, and Rayquaza are to catch them.
Like you go to the cave in Sootopolis City, and yeah.
I don't really agree on this. Having this idea is like placing Hoenn within the game, when it wouldn't be needed. Not to mention, the only way into Sootopolis is with a Submarine or Plane/Helicoptor, as their main lower entrance is underwater. So, I really don't think Game Freak will allow trainers to go back to one location in Hoenn for the legendary catch, when they have the option of simply placing them within Kanto or Johto itself, making the process much easier.