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I played the demo of Virtue on my Vita and it was definitely interesting. How important is 999 to it? I might pick up both on the 3DS if it's important.
It is. There's quite an overarching story. VLR can be treated as standalone, but I strongly suggest against it. That said, most of the worthwhile concepts and events of 999 are references (spoiled, if you will) and explained in VLR. It's your call.
Far as Vita vs. 3DS, there are pros and cons to each. In my book, the Vita version's perk is taking screenshots. Others say the higher resolution is nice, but it doesn't bother me. The 3DS's perk is using the touch screen's 'Memo pad' to record notes and solve puzzles as you go without a sheet of paper. I used it the entire time and now store passwords the game provides in it forever.
Go to Gamestop, buy a Steam card, and use it to purchase Ys Origin. You won't be disappointed. For more info: http://www.worldofys.com/yso/