In a recent interview with Game Informer Game Freaks Junichi Masuda was asked about the potential of seeing Pokemon Games hit the 3DS virtual console. As it stands it seems like this won't happen at all based on a selection of ideas which Game Freak prefers to adjust every few years. As it stands at Game Freak they see the Pokemon games in need of evolving and based on the way they play require a certain update to allow them to connect and work with modern games.
Here is Junichi Masuda's full statement about the question:
Our focus right now, as you can see with Omega Ruby and Alpha Sapphire being a good example, is with the older titles we like to go back and update them and kind of power them up for the new generation. A lot of the communication features we feel that are obviously core to the Pokémon series, we have to update them. So for example these titles are compatible with Pokémon X and Y, you can battle and trade between the two series of games. So right now it’s just really that the only reason is that our focus is on actually updating the games and doing remakes instead of putting out the old titles.