I don't really have an issue, since I can always trade to another game to keep my Pokemon, but the big problem I have is the gift Pokemon from events who have ribbons or whatever that make it impossible for you to trade them... If the promotion had ended, you can never get that Pokemon again, should you want to restart. You have to delete your event Pokemon...
I have a funny feeling I'm going to end up with multiple copies of X and Y... I have 6 B2W2 copies already... (One of each in Japanese, and two of each in English.)
I don't terribly mind buying extra copies, though I hope for sales, since used games are pretty much the same price as new copies when it comes to Pokemon... (I did take advantage of that recent Best Buy sale. lol)
But if there aren't sales (and I really wouldn't count on it, at least not too often, nor too close to release) it doesn't really help... I mean, I can pay full price... But I'm cheap and poor, I don't want to! XD
I think there's not enough aftergame content for just one file to be enough though. Maybe if they had some sort of quests where you have to catch and use low level Pokemon or something... Then you would have more motivation to catch early game Pokemon you may have passed over initially... I dunno, I'm not so into competitive battling so for me the game just ends after the story is over... I end up doing minigames over and over (contests, game corner, underground, etc.) and nothing else really... So for casual players it might be nice to at least have more motivation to keep playing, if there continues to be only one file.
I wish there was more than one file though... Because it's more fun to try and experience the adventure in many different ways. In one of my games I am doing a speed run, and in another one, I am doing a really slow run where I don't move on until I catch ever Pokemon available. lol And in some games I'm playing with a set team the whole way through, and in others I'll just catch and use whatever I feel like, and swap out for different situations, which is what I used to always do as a kid, before wifi, in the old days. XD I really think it would be more fun to play more than one file. Pokemon games, as they are now, are really short games. You can beat them, including the after game, in really maybe a week or a month, if you put in a few hours a day... But the games are much much further apart. If you aren't interested in competitive battles or completing your Pokedex, but want to still play Pokemon, what do you do? You start from the beginning... But if you don't want to lose your Pokemon, items, file, etc. you have to buy a whole new game and that kinda sucks.
All that said, I really don't expect it, after all this time, despite how much I want it... It just doesn't seem like simply moving up to the 3DS would be enough reason for them to implement it. I hope I'm wrong but I don't think I am.