Well, KidCarter, I think you might have settled a lot of the dispute going about this thread. I think the very concept of a massive Pokemon game is amazing, but with all the other games, how would they implement enough of a story line to compete? I mean, it would get VERY dull and repetitive as you go on, especially for veterans. Sure, it is a total revamp with enhanced graphics and such (I won't even delve into the storage space, because this is all merely speculation) but if you just stick in the same old stuff from the past games, the concept falls over in its own flaw.
Now only that, but we are also neglecting the spin-off regions such as those in Pokemon Ranger and maybe/probably/somewhat those in Pokemon Rescue Dungeon. Are those worth even giving a spot in the game, or are they forever to remain as spin-offs? On second thought, they would be kind of pointless, considering they would be full with the same Pokemon in the other regions. However, it wouldn't hurt to mind them a mini-game or two just to show they were there in the first place.
As said before, this would all be impossible in the current stage of technology, seeing as you'd need to buy a pre-made computer full of the game's guts to run it properly (Hyperbole, deal with it), but that doesn't mean speculation is disallowed. This is kind of enjoyable.