Ever since the first Pokemon games were released, I've been wondering why they haven't allowed more than one save file. And the answer is blatantly obvious-
It would allow the capture of all the Pokemon far too easily.
I mean, even with only two game catridges and two save files per cartridge, one could easily capture the three Legendary Dogs on FR/LG, obtain the 3 Johto starters from Emerald,etc etc.
Not only that, but as AkariKanzaki said, it rakes in more money for them. After all, they ARE a business, and the whole point of a business is to make money.