I really think they will do what emerald did to the johto starters.
Once you catch the 251 pokemon in the johto dex, you can get one of the Kanto starters, and something else could happen an you could get the hoen starters, I really don't think they would leave 6 or even less pokemon out of the games, that would just be dumb.
Mewtwo will end up in its cave.
The Lati's will end up roaming, perhaps by game, gender, or even choice like in Emerald.
Groudon, Kyogre, and Raquayza have been confirmed, but idk where they will end up in the game, that stumps me.
Celebi will be an event, end of story.
As for your post "a person" That would be a good idea, since this is one game that allows you to get both "box" pokemon, it would give you incentive to choosing one over the other.
The dogs will remain roamers, no matter what, but perhaps based off of your starter
-Cyndaquil-Suiccune
-Chikorita-Entai
-Tododile-Raiku
the Crystal story could occur, but off of any of them. <-- Ik many of you will bash this idea, but it would add more depth to the story.
That covers all unobtainable pokemon throughout the games w/o GBA transferring. I might have missed plain wild pokemon, but they will more than likely pop up in some wild place.