The good news is the makers of Shoddy would ideally like to implement this.
The bad news is that it doesn't seem to be a high priority for them and I doubt it'll happen before the 5th generation of Pokémon comes out.
The good news is that Shoddy is open source, so if you know Java, you could implement this yourself.
The bad news is that the existing code of Shoddy is not conducive to Double Battles. A lot of it uses shortcuts, for lack of a better word, that assume the environment is Singles.
If I were you, I'd stick with Wi-Fi.
EDIT: Also, Shoddy has its own forums. You should really post this sort of discussion there. Smogon isn't in charge of Shoddy Battle.