A way this could work could be a single program that offers both versions through the program. If this is done, then an extra option to trade from one game to another could work, but it kinda takes the point out of trading...
Also, something like the yellow version setup to get all starters and then a game with every pokemon in it could work, trading could still be used, but unnecessary...
I think the best solution however, would be to make a seperate program that can take game data and allow you to enter online trade/batle areas. the program would obviously be on a computer for internet, but it allows real community feel, no metter where you are. If this was done, it shouldn't replace
zune to
zune trading/battling however because you can't do this on the fly and if you do happen to have a friend with the
zune it could get annoying to have to use computers to trade/battle each other instead of being able to do it during a passing period at school or something...