Was just talking in IRC and came up with a few ideas:
In Gen 3+ there was the part in the Pokemon Center for Multiplayer and in a room you could select your position for double battles. Maybe that's how battling each other in-game could be solved by having set position marks?
And for Co-Op battling it could be like in Pokemon Platinum where certain areas you would get an escort (or you would have to escort someone) through a forest and there were double battles there whilst you had a partner. There is also the option of bringing in the special tall grass from Gen 5 where double battles happen frequently.
Now these are random ideas and the second I think breaks the original game formula more as it was never designed for it but again, just an idea
In Gen 3+ there was the part in the Pokemon Center for Multiplayer and in a room you could select your position for double battles. Maybe that's how battling each other in-game could be solved by having set position marks?
And for Co-Op battling it could be like in Pokemon Platinum where certain areas you would get an escort (or you would have to escort someone) through a forest and there were double battles there whilst you had a partner. There is also the option of bringing in the special tall grass from Gen 5 where double battles happen frequently.
Now these are random ideas and the second I think breaks the original game formula more as it was never designed for it but again, just an idea