Do you own both consoles? Which do you play more? I actually think that both of these handhelds are pretty great and I play both pretty regularly, but both have different functions for me.
The PS Vita operates as something of a 'in-case-you-missed-it' machine. I use it to play all of the indie games I never got round to playing. I played Hotline Miami like this, Spelunky. I went back to games like Fez on the PS Vita. It's actually a gorgeous device, with a beautiful screen and a growing library of brilliant, sexy games.
The 3DS? It's a beast. It has so many legitimately incredible games. My top two favourite games of last year were on the 3DS: Luigi's Mansion 2 and A Link Between Worlds.
I'd say if I had to choose one of the two, I would choose the 3DS. But the PS Vita? Man. I love that console and it needs way, way more love.