We here at PSLS love our Vitas, hell we’ve played all the games on it, but there’s one thing that really bugs us – that game saves are tied to the entire game data of a digital title, so deleting one deletes the other.
That means if you’ve been playing some Uncharted: Golden Abyss, make it halfway through, and then decide to delete it so you have space to play something else, you’re going to have to lose your savedata as well – resetting your progress in the game. In comparison, the PS3 and PSP have separate save folders, so you can delete Flower, but keep the savedata and come back two years later to pick up exactly where you left off.
It’s not all bad – you can backup the data, but that requires you to backup the whole thing, taking up precious space on your PS3, PC or Mac. And even if space isn’t a concern, it’s pretty silly that you have to use a static device like a PS3 to make your portable work fully. Additionally, the Vita can support separate savedata for the PSP, so it does seem like the software is capable of supporting separate savedata:
Hopefully this isn’t a problem that’s unfixable, and rather one that will be amended in an upcoming firmware update – along with a few more fixes.