GBA Virtual Console would have to be reworked significantly for Pokemon to work.
Currently, the GBA emulation functions the same way a DS game does rather than like other titles. No returning to the menu unless you quit the game, and for official VC releases, there's a significant amount ghosting and the screen is darkened. In Pokemon's case, RSE and FRLG have two saves, the current/most recent save and the backup save in case anything goes wrong, making the save size bigger than anything the GBA VC is capable of handling. If one were to remove the backup save mechanic to make the games work, you would always be greeted to a "save is corrupted" message when starting up the game.
