They are 3DS games, and the 3DS doesn't have a GBA slot. The only way they'd directly connect is if they had something to transmit to an original DS or DS Lite though Download Play, which would then grab Pokemon from the GBA games. And that seems... mostly pointless. Especially since it hinges on people having a functioning DS or DS Lite, which fewer and fewer people have.
I can't really see this happening. Pokemon is all about player interaction - trading, battling. Remember the old slogan - gotta catch 'em all?
Putting them on the Virtual Console would essentially remove the possibility of multiplayer. Not only could you not complete the Pokedex, because of version exclusives, you also couldn't even evolve all the Pokemon you can catch, because of trade evolutions.
Pretty much the only way this would happen is if Nintendo was desperate enough for cash that they'd bother essentially completely rewriting how the game handles multiplayer to handle 3DS wireless.