I'm not sure who exactly is going to be making anymore 3DS games though
Looking at Nintendo's 1st parties we have
EAD1- Mario Kart Wii U
EAD2- Just Finished Nintendo Land and Animal Crossing, probably starting on a Wii U animal crossing
EAD3- Possibly could get Zelda out there for 3DS, but I don't think it will be ready until next year, and if it is revealed at E3 I don't see it being released the same year
EAD4- Still can't get Pikmin 3 out the door, also just finished NSMB2 and NSMBU
EAD5- Wii Fit U is going out the door this year
Intelligent Systems- Just finshed Paper Mario, presumably working on Fire EmblemxSMT, maybe enough staff for an Advance Wars or new IP?
Monolith- possible 3DS game could be out in Japan this year, but no way it is in America or could be considered a holiday game
Camelot- Mario Golf
Retro- probably understaffed as it is for their Wii U game
Good Feel- Yoshi Land
Alpha Dream- Mario and Luigi
EAD Tokyo- 3D Mario Wii U
Next Level- as long as it took to get LM2 out...no
The big one I haven't mentioned is Monster and they could possibly have a new racing game which is believable
Treasure is working on a 3DS game which might be co-developed with Nintendo like Sin & Punishment 2.
Creatures Inc. who worked on the Poképark and Pokémon Ranger games could have something for 3DS. Their games are shit though.
HAL is probably working on Kirby for the 3DS.
IntSys is also working on Game & Wario for Wii U so depending on the scope of FExSMT and Atlus' involvement I think it'll be a while until they release a retail 3DS game. For all we know they still could have a team working on a 3DS game. Or not.
Brownie Brown/1-Up is helping with a game as well, most likely for 3DS.
Grezzo could be doing the grunt work for Majora's Mask 3D (assuming it exists).
Looking at the scale of X, Monolith working on a 3DS game as well, at least in any meaningful capacity, seems unrealistic. Unless it's the Project X Zone team.
Monster I'm not sure about. They don't seem to be big enough for HD development but it's hard to really know. Finger's crossed for F-Zero I guess.
Genius Sonority's output has mostly been Pokémon games or some small-scale stuff. I think they might be working on a Wii U companion game for Pokémon X&Y.
Paon seems to be a safe contender but they haven't developed any games for Nintendo in a while.
So basically everyone is working on iterations of the same franchises over and over again.
I don't see Mario Kart or Zelda saving the WiiU. A price cut should help it down the line, but ultimately we're looking at another Gamecube situation where Nintendo is isolated from the rest of the market, and in last place. The system will get plenty of 360 ports but next gen games will likely be focused on the PS4/next Xbox, meaning there will be very little incentive or reason to buy anything on the WiiU outside of Nintendo games.
Nintendo had a small window of opportunity where they needed to sell a lot of hardware and reassure third parties. That window has virtually closed with the PS4's reveal on the horizon, and no new (or big) WiiU games coming out soon. This thing will limp until it gets a price cut imo. If the PS4/next Xbox don't launch at some ridiculous price, I honestly think the WiiU will be finished.
It'll be interesting to see how this E3 plays out for them. If Mario Kart comes out this year and doesn't turn it around somewhat, the console is done.