Well, I don't remember when it was, but SE has said some time ago they wouldn't do anything with the game, they didn't wan't to ruin the game with a bad sequel (well, Chrono Cross isn't exactly a sequel), I doubt they'd seriously consider changing the changing the whole game, and if they did, I doubt they'd put it on a portable system like the Vita or 3DS, but rather the WiiU or PS4, which I highly doubt either...
In order to make the game fully 3D, they'd have to change the whole game, and that is something that could go terribly wrong, some games just don't work well in 3D.
Dragon Quest remakes are pretty much released only for the Nintendo handhelds nowadays, so that isn't a choice either, as for Final Fantasy, most remakes have been for Nintendo too (plus, I read somewhere that SE was considering a FFV remake for the 3DS if the console sold well), so I don't see much from there either, although Sony usually gets new games instead like Crysis Core, Dissiada and Type-0 IIRC, so they could be making a new game along those lines.
One game that I imagine SE will release for the Vita is some sort of Kingdom Hearts, the series have been spread between Sony and Nintendo handhelds, so I imagine they'll continue doing the same. I can see a KH game being a system seller for a lot of people, especially if it comes with new stuff.
I don't really see the Vita as a commercial failure, it is facing pretty hard times, so developers are fearful right now, once it gets a bit of momentum I'm sure it'll get more games, kinda like the PSP.
Although it'll probably never surpass the 3DS in terms of sales, since that'd be pretty hard.