To be fair, the very idea of playing as Aqua in the Realm of Darkness suggests interesting things about the story. For one, it'd almost have to be more psychological, given that there wouldn't be a lot of real people around for her to interact with. For another, it'd be focused on someone in an incredibly precarious position both physically (due to the constant threat of Heartless attack) and mentally (due to isolation added on top of everything Aqua's been through already), which would easily translate into the sort of tension KH doesn't normally do.
That's a good part of the reason why I'd absolutely love a BbSv2 but wouldn't be all too pleased with another game before KH3 -- there's just so much potential there that doing anything else would pale in comparison to what could have been (especially because there isn't much room for anything else without unnecessary retcons).