Things like Battle Tower would also need to be thought about carefully. Would the BT's be as they currently are and once all the region's have been completed, there's a separate island (possibly where the best trainer tournament, as mentioned in my last post, would be) where the battle frontier would be and then all the previous BT's close down and redirect to there instead. Or would they simply be kept in there original places with no changes to that part of the game?
Graphics, as you mentioned, would also be a major part because if they were to use the latest Pokemon graphics throughout the whole game, that could be a turn off to some people because they may not like the latest graphics and want more of a nostalgic feel to it.
I reckon just from such questions, aswell as inevitably tons of others, is the reason why it's highly unlikely to ever happen. All the community needs to wait for is the technology to be available and then it could be a huge community project to create the ultimate game.