3DS is superior in terms of current content (Bravely Default and Fire Emblem Awakening alone put it ahead) but the Vita is catching up fast, and I believe it'll take over the 3DS as the primary JRPG console soon, with games like Demon Gaze (kind of like Eterian Odyssey) and Conception II (kind of like Persona, just a little more niche) coming out soon, along with excellent games like Ys Memories of Celceta and Persona 4 Golden already out. I personally would go with 3DS for the current selection, but if you are willing to let the game market mature I would go with Vita. Or, get the best of both worlds and get a 3DS now, and get the Vita a year or two down the road.
Note: If you want to get an OLED Vita (superior screen), you'll have to get it now though, they are being discontinued. The LCD screen of the slim isn't that bad though, so it's nothing to worry about if you do go witth the 3DS.
Edit: I personally find myself playing my Vita more than my XL these days, but Bravely Default is my favourite JRPG since FFIX, forced extended gameplay or not. Plus Bravely Second looks like it's gonna kick ass.