I happen to own both systems and to me, the Vita is also better. There's no question about hardware, it's always hard to get back to the 3DS XL with it's inferior displays. You can count every pixel even meters away and the colours don't even come close to the Vita. This also effects apps such as the browser, which is as good as useless on the 3DS but pretty good on the Vita.
Of course hardware isn't a deal breaker, but on the games side, I also see the Vita in advantage. I'm having a hell lot of fun right now with Killzone: Mercenary, there simply isn't any shooter on the 3DS that could compare to that. The gameplay is a blast with two real analog sticks, it's just like a shooter is meant to be played. And the graphics, oh my god, I didn't knew something like that would be even possible on a portable.
Dead or Alive 5 is also on of my favourites. I also have Dead or Alibe Dimensions on 3DS, which is fun, but doesn't come close to the Vita version. In direct comparison, DoA 5+ is better than DoA Dimensions in every single aspect.
Of course Metal Gear has to be on my list, with the HD collection, that I got free from Plus, being much much MUCH better than Snake Eater 3D, which was hyped like hell when 3DS was announced. First off, the graphics are horrible. It looks decent, but it stutters like hell. Then the controls are just bad. You need that second stick for MGS3. The Vita version is better in every aspect and offers more content on top while being cheaper. If you have both 3DS and Vita, it's a no brainer which version to get.
I bought the 3DS mainly for Nintendo games. I got the Animal Crossing Special Edition and that game is also my favourite game for 3DS. There's nothing comparable on Vita or on any other platform. I enjoy it quite a lot, every once in a while, I don't want a challenge, I just want to sit back and relax, maybe hang out with friends. Only thing that sucks is the text chat. It happened to me that I played Animal Crossing with a friend while we talked via the Vita party chat. I'm not kidding.
The first game I then bought was Super Mario 3D Land. It's fun and all, but lacks really new ideas. As I played nearly every Mario platformer there is, it can get boring at times. It's also a very short game, it took me no more than 4.5 hours to get through. Sure, there are additional challenges, but I'm not really motivated to get into them.
I also bought Donkey Kong Country 3D which I enjoyed a lot. I also have the Wii version but didn't like that at all. That wiggling with the wiimote really turned me off, precise gameplay is impossible with that. Luickily, on the 3DS, that is no more, Just buttons, no wiggling. Thanks to that, I played to the end of DKCR for the first time and enjoyed it quite a lot. Not a game on Vita that could compare.
I have Fire Emblem, but I didn't get warm with it. It's just so simplistic, even more than XCOM: Enemy Unknown. Most times the missions are just too easy which isn't fun to me. Maybe i gets better later in the game, I don't know.
What I do like about the 3DS is the Gameboy Emulator. It's the only thing where I use the 3D function. I turn on that Gameboy borders and the green colours and oh boy, it looks just like a real Gameboy thanks to 3D!. Easily the best Gameboy Emulator around. But the games are waaaaaay too expensive.
On the Vita, you have so much games that are just not possible on 3DS. The Walking Dead is easily one of the best games I have ever played and it's on Vita. All the best indie games are released for Vita or they are on their way to the system, even Minecraft. Sure, you can say you hate all indie games, but that would be like, a little biased? Hating everything without even trying, just because it's indy and all?
Overall, I find Vita games to be much deeper than 3DS games. The better tech with better controls and better graphics are just the icing on the cake. Because of the much much better online functionality, many Vita games also offer nearly infinite replay value thanks to multiplayer modes. While with something like Mario, you play it once, maybe even do all challenges, and then never touch it again.
And as a last point, PS Plus is a plus (literally) for Vita. It leads me to trying games I wouldn't have touched otherwise. While on 3DS, I have to pay 40 € just to try a game. Also, I spent around the same money for Vita games than for 3DS games, but I have 20 games for Vita and only 8 for 3DS. With plus, you spend less money and get a better value than on 3DS.
All in all, the Vita is a better system in every aspect, if you ask me. That said, if you like Nintendo titles, theres no way to avoid a 3DS. I all comes down to personal preference when it comes to games. But in terms of hardware, thre Vita crushes the 3DS. Not judt in specs, but also in built quality, comfort and design.
Official member of VGC's Nintendo family, approved by the one and only RolStoppable. I feel honored.