Well one reason for a single save file is so siblings or friends can't share a copy. A bit dirty but eh.
Personally I don't care for two save files. If I start again it's to start again, I don't need my old file. Though it wouldn't hurt to have a Pokémon box or ranch or something on the eShop that can store your Pokémon from different save files and games, so that you could keep your collection even if you delete a save.