No, you cannot have two save games on one copy of a game in any Pokemon game. It is possible to make a temporary game without deleting your save, but you can't save that game if you already have an existing save game.
If your talking about 2 save files in the same cartridge or online purchased game, no. One save file per game. You can have two save files with one cartridge and one game that you bought online (Nintendo e-shop). My source: past experience (sadly)
no you cant you can have that in the gba games butt no 3ds
hope this helps