I have both, "I personally" like my Vita more than I do my 3DS.
My Vita has more features and more games that are appealing to "me".
My 3DS I only bought for Pokemon, Sonic, and Smash. It also has less features and is overall not "my" cup of tea.
Both systems are great, but what defines them is what you have a taste for. I would recommend both to anyone based on their preference when it comes to mobile gaming.