I bought both.
Vita: was honestly the biggest waste of $ I ever spent. I bought it at launch and has a whopping one game Uncharted: GA and after about 4 months of dust collecting I traded it in for a 3ds XL
Vita: 50/100 First impression was that it looks really nice and I like the control sticks.
3ds: Ive had this for a little over a year now and I have played it nearly everyday. With a massive 130+ hours into Ocarina of Time I can pop that game in anyday. I also have Mario Kart 7 and Pokemon X both fun to play online every once in a while.
3ds: 90/100 Very nice system, does not look as cool as Vita though. Oh yea it has youtube now and it is great also.