Multiple save files do not bring up the possibility of cloning, only of obtaining all three starters and multiples of each legendary.
Which you could do anyway by trading them off and restarting. Multiple save files simply allows you to have a bout of "you know what I really wanna play again? Pokemon!" without having to restart your file. To this day I don't have the heart to restart my Emerald, but I've wanted to plenty of times.
As for the actual discussion, I think PC boxes saved on the SD card is a definite possibility. It makes the lives of the living Pokedex people (like me!) much easier when the living Pokedex is no longer competing for space with your competitive Pokemon, your sentimental Pokemon you caught in 2003, the multiple one-off Pokemon you've accrued over the years. The number of sentimental, one-off, and competitive Pokemon that need to be kept seem to increase faster than available box space does.
A two save file thing would be cool, with a twist. Perhaps one save file is the protagonist that beats the Gyms and becomes Champion, while the other is the protagonist that goes after the evil team. Events finished in one save file effect the world in the other, as if the two adventures are happening concurrently. When both files are completed, the Pokemon and post game are merged, so you can pick whichever protagonist you like better and head through the post game with them.
That'd be something I'd love to see.
Off-topic: I'm still waiting for that GBC hack you don't do betas for Jeremy :P. It's good to see another familiar face from when I first joined the hacking scene!
