I have both and both get played fairly equally. I've got way more 3DS games than Vita games, but I'm lately finding myself underwhelmed by Nintendo's offerings and if you asked me what the best 3DS game is, I'd say Resident Evil Revelations and that just hit consoles. Nothing in the 3DS library is better than Persona 4 Golden IMO. But games such as Fire Emblem, Professor Layton, and inevitably Ace Attorney 5, make the 3DS a good system.
"Hairy Zeus on a traffic light!" -Deadpool, Issue #3