I don't like recommending games without knowing what a person likes. If you don't like a certain genre than its pretty rare that a game in it will suddenly appeal to you when others failed.
That said, I'll give you a quick ranking of some games I've played recently.
Rhythm Thief and the Emperor's Treasure - It's not a perfect game and it can frustrate but it was right up my alley. A combination of Professor Layton, Rhythm Heaven and Sega flair, I dug the story, I dug the characters, the setting, the music and the different minigames even the gyro ones. Still my favorite 3DS game.
I'd recommend AC: New Leaf but I know you've got already.
Super Mario 3D Land is one of the better Mario games I've played in some time but it is a different kind of 3D Mario game. Some people dig it, some don't. I did but I'm not over the moon about it like say Insanolord.
After that, these are use your own discretion games:
NSMB2 was a disappointment to me. I found the game forgettable and the coin challenges not my cup of tea.
Rayman 3D is interesting if you've never played Rayman 2: The Great Escape before. I hadn't and playing it with the 3D effect was nice. It shows it's age as it was released back in the N64 days but despite some odd glitches, I was happy enough with the purchase and package.
Pilotwings Resort is OK if you crave some piloting action. It's just very mission based. Even the free-roaming part of the game keeps you on a time limit and you are supposed to find and locate various things all over. Plus, the limited setting can make things a bit repetitive. Playing some missions where you have to shoot targets made me realize how much I'd like a new Rogue Squadron type game with actual aerial combat. It was another game that highlighted the usefulness of 3D compared to 2D and I couldn't go back to 2D when playing it. Pleasant but it could be frustrating if you want to get perfect mission scores and not too much depth.
Mario Kart 7 did not hold my attention for long. I got 3 stars for all the 50cc cups and was working on the 100cc when Animal Crossing took over my life. I'll go back to it at some point but even now when I think about it, I'm not thrilled about the prospect. It just felt bland and I can't even remember half of the courses at this point.
Donkey 94 was similar to Mario vs Donkey Kong. I was disappointed because it gets hyped on this board like something special but I found it very close to MvsDK and therefore it was a "meh" worthy game.
Super Mario Land 2 is likewise a disappointment. It's one of the weakest Mario games I've ever played and despite the first Land being less conventional, I prefer it more than this game.
Metroid 2 is also not as I had imagined or hoped it to be and my interest in it faded soon after playing it.
I'm close to finishing the first Pushmo and it is definitely worth the praise. Sometimes I wonder if I'm solving the puzzles right as the solutions seem a bit odd to me but maybe that is the game messing with my head. I do find I enjoyed it a bit more when the puzzles were easy but now that they are harder at the end, I usually want a break after 3 or 4. Don't know why that it is.
So, not much on the Eshop for me to recommend.
Other than that, I've been playing some Wii and DS games but you only wanted Wii U and 3DS game recommendations.
I know Kirby Triple Deluxe is supposed to be really good and I've bought it with the expectation that I'll be playing it next when I catch up again in my New Leaf gameplay. If you like Kirby games, it does look pretty stellar.
Personally, I'm going to be buying another game myself as I've got a $15.00 off coupon to use. I'm just not sure if it will be Mario Golf: World Tour, Zelda: A Link Between Worlds or The Wonderful 101. I just mention it as it gives you an idea of games at the top of my purchasing radar.