Depends on your preferences. If you’re into JPRGs (which I do believe you are), the 3DS will always win. Vita’s library has grown significantly since its early years of drought, but it’s still not big on exclusives. I’d say it’s worth it for games like Persona 4 Golden, Gravity Rush, Ys: Celceta, FFX HD Remaster, Danganronpa, Soul Sacrifice, etc. though. There’s also a huge library of PSP, PSOne and indie games to consider.
In terms of hardware and ergonomics (imo), the Vita wins by a country mile. Plus, it actually has a real account system which means you can go all digital without fear.