There is a reason there's only one save file: the PC, more specifically the possibility to nickname every single Pokémon. It's a LOT of data to save. Plus, there's also all the usual data: flags that mean you've defeated trainers, picked up objects etc.
It doesn't matter if you get a physical copy or a digital one on your SD card: the save files are always capped at a certain size. With a physical copy, it's a hardware issue: you only have so much space for the save file (and no matter what Pokémon X/Y says, it saves to the cartridge, not the SD card) . With a digital download, there are two reasons: first, they clearly don't want people with digital copies to have a better version of the game than those who bought carts; second, there's a technical choice of allocating limited space to save files to avoid a game slowly overtaking the entire SD card when you save more and more stuff.
Let me put it this way: two save files means a Pokémon game can manage and save half the data it can manage now. Which means every game mechanic and piece of content that needs to save data becomes cut in half: you'll get two times less trainers, items, PC boxes, various secrets...
So no, I am pretty sure I don't want multiple save files par game... in the same way Zelda manages them, at least. What I do want is a way to freely back up and restore save files.