After the DS lite ends in trash-cans and gets replaced by the DSi after a few months, the following Pokémon will be unobtainable (if you own D P and Pt you can get all the others ingame):
The starters from the past 3 gens was obvious, as were the legends (except regis and birds which are in platinum)...
So. The least problematic ones are the hoenn guys, as they're not that many years away yet.
With GS DS, the Johto starters, legends, tediursas shuckles and pinecos are solved.
And if aynone can remember, there are kanto pokemon in Johto too, such as vulpix,sandshrew,ekans,growlithe,caterpie and weedle to name those which are missing in 4th gen DSi era games. Which are all the Kanto ones =)
With that, the most rare would be Mew, Kanto starters and Mewtwo... Mew needs another ingame event place anyways. I can absolutely imagine the SS anne taking you to faraway island after getting the event ticket =)
For the starters...hmmm... there are many ways how they could make you obtain a kanto starter in the 3year-future GS kanto.... maybe oak would give you one, or ...hey what about the guys from yellow who gave you the starters? kanto will get alot of new stuff anyway IMO to make up for the crap it was in GSC. Too continoue my speculation, put da Mewtwo in it's freakin cerulian cave =D
Then the rarest pokemon species remain Hoenn stuff...
In sinnoh there's a pokeradar, swarms, safari daily pokes, trophy garden... all of those features like doubled the pokemon you can find in DPPt
In Johto the swarming pokes were invented! there's a bug catching contest where there could be a daily bug poke from a different region D:
and of course: "there's a zangoose swarm on route 45 today!" .. or ... "seedot swarm at Ilex forest" etc
All that text makes me wanna play those GS remakes xD