Don't own a 3ds so I can't speak for it but the Vita sure has it's fair share of JRPGs like:

Persona 4 Golden (Highly acclaimed as one of the greatest in it's genre)
Ys: Memories of Celceta
Final Fantasy X|X-2 HD
Atelier Meruru Plus: The Apprentice of Arland
Conception II: Children of the Seven Stars
Demon Gaze
Disgaea 3: Absence of Detention
Dragon Fantasy: Book I
Dragon Fantasy: Book II
New Little King's Story
Ragnarok Odyssey
Rainbow Moon
Sorcery Saga: Curse of the Great Curry God
Soul Sacrifice
Valhalla Knights 3

Dragon's Crown

Not to mention everything from the PSP and PS1 library.

Anyone who actually picked a side is wrong.
If you truly are a fan of JRPGs both of these handhelds are a must own.
PSVita has PS1, PSP and the Vita's JRPGs which often are more niche however there is the occasional large title.
3DS has DS and the 3DS JRPGs which are often more well known like Dragon Quest or Kingdom Hearts.
Both however have too many amazing games stuck in Japan, so you best start learning Japanese now.

And the 3DS is region locked too :(

well, when it comes to RPGs onlye, ps vita is far superior than 3ds, but as somene said, a lot of psvita's rpg are very niche.

....I think the 3DS has more original games so far.

The Vita has very well made ports (FF X HD and Persona 4 Golden, Atelier titles) and a few original titles on the horizon like Demon Gaze.

So if you had to choose between them and JRPGs are the only games you play then...yeah, the 3DS would be the better choice

...but there are so many great games on both systems which are worth playing, so you can´t go wrong with either of them and I´d advise to buy both eventually.

since you're think of getting a vita, i'd say go for the vita as it has a good mix of RPG's

you have your basic turn based RPG's like Persona 4 and FF X/FFX-2
your side scrollers like Dragon's Crown and Muramasa(yes technically it's and RPG)
action RPG's like Soul Sacrifice/YS: memories of celceta/Toukiden

and some of the games I mentioned like Dragon's Crown/Soul Sacrifice/Toukiden also support multiplayer as well

plus much of the PSP/PS1 library as well

That's also coming out for 3DS soon so that kind of cancels out.

Honestly you cannot go wrong with either, much of it comes down to personal taste.

Vita probably has the better one, but 3ds has Etrian Odyssey so...

I did not said it works on Vita buddy, read my post again. I saidthat the PSP have the best RPGs, never mentioned Vita.