The whole bug business in the US version aside, I would definitely recommend the 3DS version over the Vita version, because of three reasons
I want to try the 3DS demo first before committing though, it'll feel more at home on that console imo.
1) Notes are easier to take and reference while solving puzzles and this is really helpful
2) The 3D helps you distinguish where to move, where things are in the puzzles environments more easily, while sometimes, not often, but sometimes on the Vita they blend into the environment
3) The touch controls are better and more responsive on the 3DS
Whether the game looks nicer is down to whether you like the 3D or the Vita's amazing screen better, I think.
This is a compilation of what people have said, plus hands time with the Vita version after I won the 3DS version.
If anyone is still debating on which one, I can answer other questions to help you make the choice. Don't miss this game, its truly a worthy followup to 999 and a really smart example of how to do a modern adventure game. I kind of wish some PC developers would play it and get inspired.
Edited by JinTypeNoir at 12:00:30 05-11-2012