I posted a huge list on a similar topic this month, but I'll cut it to what's being worked on now. Note that if there is another restructure or change in heads and whatnot, we'll probably find out when the next FY starts.
EAD Kyoto Group 1 (Hideki Konno) - Mario Kart U [Early 2014], Assistance in Luigi's Mansion: Dark Moon [Early 2013]
Reasoning: They developed Luigi's Mansion and might have some assistance for Next Level Games, at least during preproduction. Meanwhile, Mario Kart U would be great for next holiday, but they might have too much out on Holiday 2013 and delay this sure-hit for the following Spring, a la MKWii.
EAD Kyoto Group 2 (Katsuya Eguchi) - Animal Crossing: New Leaf (US/EU) [Late Spring 2013], Wii Sports U [Holiday 2013/2014]
Reasoning: Animal Crossing is Q2 in EU, probably similar for US if not, Summer. Meanwhile, we've seen videos of Sports games since Wii U's unveiling, so it should see a release at some point. Might be a good casual hit for holiday 2013 to combat Kinect 2.
EAD Kyoto Group 3 (Eiji Aonuma) - New 3DS Zelda [Holiday 2013], Wii U Zelda [Holiday 2014/2015]
Reasoning: With GREZZO working on the previous handheld releases, I suspect that some of this team has been able to work on a 3DS adventure. It would really help the 3DS's next holiday, for sure! Console Zelda probably needs 3 years between releases to be finished.
EAD Kyoto Group 4 (Hiroyuki Kimura) - NSMBU DLC [2013], Pikmin 3 [Q2 2013]
Reasoning: No way any new game from Group 4 will be known until 2014 at the earliest. Looks to be about 2+ teams now, so I suspect a team shuffle to other EAD groups or another 3DS project for 2014/5.
EAD Kyoto Group 5 (Tadashi Sugiyama) - Wii Fit U [Q1 2013], Collab Project 3DS [Late 2013/2014]
Reasoning: This team appears to be the smallest group at EAD, and Wii Fit U is expected for early early 2013. Looking forward, I see another collaboration for either late 2013 or 2014, most likely 3DS related.
EAD Tokyo Group 1 (Takao Shimizu) - ???
Reasoning: This team of EAD Tokyo is a mystery to me. It seems the team is fairly small and acts like Kyoto Group 5 in nature. I suspect GREZZO's next project is being co-developed with them, most likely 3DS related. Don't expect a new IP here unless we have all been tricked with their inactivity.
EAD Tokyo Group 2 (Yoshiaki Koizumi) - Wii U Mario Title [Holiday 2013]
Reasoning: Super Mario 3D Land was developed pretty quickly, especially considering the earthquake tragedy. I suspect Nintendo will not let this miss Holiday season, and it might be getting assistance from other developers to make it out in 2013. If other big games hit instead, it will be mid-2014 a la SMG2. New IP is not going to happen.
SPD Group 1 - Game & Wario (w/ Intelligent Systems) [Q1 2013], Tomodachi Collection 2 (JPN-only) [2013]
Reasoning: WarioWare-like games have been made consistently by this team, and Tomodachi Collection 2 has been teased too often for it NOT to miss 2013. The latter will never hit US but will sell better than G&W WW could ever reach.
SPD Group 2 (Hitoshi Yamagami) - Wii U Monolith Soft title [2013]
Reasoning: SPD is hard to figure out, really. But if I had to take a guess I imagine they are working on another Monolith Soft game and perhaps another 3DS title with an outside dev.
SPD Group 3 (Kensuke Tanabe) - Luigi's Mansion: Dark Moon (w/ Next Level Games) [Spring 2013], Next Retro Project [2013], Next Monster Games Project [2013]
Reasoning: Tanabe's team mostly works on western-developed releases as a support team. Knowing this, he probably is assisting in LM2, although less so with Miyamoto on board. Retro and Monster Games are certain to have new games coming very soon.
SPD Group 4 (Hiroshi Sato) - Mario Party U (w/ Nd Cube) [Late 2013 / Early 2014], Next Camelot Project
Reasoning: This team focuses more on publishing Japanese-developed side-projects, known for working with Camelot's games and, more recently, Nd Cube. With the latter now fully-owned by Nintendo, they might pull back a little from helping, but not at the moment.
SPD Group 5 / SDD (Masaru Nishita / Shinya Takahashi) - Brain Age: Concentration Training (EU/US) [Feb 2013], Jam with the Band 3DS [2013]
Reasoning: I suspect this team is still in existence, considering there are new entries in the team's biggest franchises coming out. One recent JPN 3DS Nintendo Direct stated that Jam with the Band is coming, so expect that within a year I'd say.
Intelligent Systems - Fire Emblem: Awakening (US/EU) [2013], Game & Wario (w/ SPD 1) [Q1 2013], Potential Wii U Ware [2014]
Reasoning: Obvious stuff here. As for another project, that can be possible, but the team just finished a handful of major projects this year. Expect more news late 2013 for a 2014 release at the earliest.
Monolith Soft - Wii U RPG [Late 2013 in Japan], New 3DS Project [2014]
Reasoning: Iwata mentioned in a Nintendo Direct that Monolith Soft ware working on something for Wii U, and it has been ~2.5 years since the last major release from them. I say Japan-only because lol, translations. Hope we don't need another Operation Rainfall this time. Also, the new Kyoto branch is working on something with Nintendo for 3DS but is a bit early yet.
Nd Cube - Mario Party U [Late 2013 or 2014]
Reasoning: With Hudson employees and some team-building, it should be big enough to work on their next project fairly smoothly. I doubt we'll see another Wii Party, after poor US reception.
Retro Studios - New Wii U Title/IP [Holiday 2013]
Reasoning: Some rumors say Retro pulled a teaser trailer from E3 at the last minute, and Reggie has said they are working on something soon. If it misses 2013, I'd say something really bad happened at Retro that we don't know. Keeping positive. Also, rumors speculate that early 2012 there was a second project started, but I'm not holding my breath.
Nintendo Software Technologies - ???
Reasoning: This company is probably working on VC stuff for Wii U and 3DS now, but with one of the creators of Sonic on the team, I also suspect they are working on a new game, whether it is a new IP (doubtful) or a handheld adventure (Donkey Kong Country for 3DS/Wii U anyone?). All speculation. I suspect a 2013/2014 announcement for their next big(ish) project.
HAL Laboratory - 3DS Kirby Title [Early 2014], Possibly Wii U Kirby Title [2014]
Reasoning: HAL tends to work with side developers on the handheld Kirby games now, and after the relative success of RtDL, I think they'll move smoothly to another console Kirby. Note that they also work on OS stuff, too. A handheld Kirby game might be faster to develop, so 2013 could happen with Engines' help.
Brownie Brown - Fantasy Life (US/EU?) (w/ Level-5) [2013?]
Reasoning: This team took forever to release this game with Level-5, and it finally releases in Japan this year. A US release can be assured at some point, but knowing L5's localization speed, I don't know what to think. More support, too?
Creatures, Inc. - Pokemon 3DS adventure or a Pokemon Wii U adventure [2014]
Reasoning: PokePark 2 is only about a year old, so whatever project they are releasing will be at least a year off...it might his Japan late 2013, but America is not going to happen.
Game Freak - HarmoKnight [Early 2013], Next Pokemon Game [Late 2013 Jpn, 2014 US/EU]
Reasoning: There are multiple teams at Game Freak working on Pokemon content, and I suspect the other team has been working between HarmoKnight and the next Pokemon game (not a remake) for 3DS. Whether we see this next year or not depends on how desperate the situation gets before mid-2013.
AlphaDream - ??? [2013]
Reasoning: Well, the website still works, so I assume they are still alive. They also apparently got a patent on a two-screen gameplay gimmick. I suspect this may turn into a 3DS adventure, but with 2+ years since the last release, I think we'll be seeing a Wii U or big 3DS game 2013 or never.
Ambrella - New Pokemon Adventure [2013/4]
Reasoning: It's Ambrella. They only do Pokemon spin-offs, and Rumble Blast did 1+ Million, so they are doing well.
Arika - ???
Reasoning: Arika has a close relationship with Nintendo, but for now, it is hard to see whether they are working with Nintendo at the moment.
Camelot - New Mario Sport game [2014]
Reasoning: Tennis Open was quickly developed, but I think the next project will be in the oven longer...not to mention it could be on Wii U, too. A mystery, this one.
Genius Sonority - The Denpa Men 2 (US/EU) [Probably mid-to-late 2013]
Reasoning: GS had been apparently been working on a big Wii RPG of sorts, but since then the company has shrunken considerably. I'm not sure Nintendo is even assisting the company that much anymore...so expect them to be reduced to pretty-cool Downloadable Games. No Wii U project expected.
Good-Feel - (shot in the dark) Yoshi's Land? [2013]
Reasoning: G-F has been good with Nintendo lately. Wario Land was an okay-seller, but KEY did very well! Knowing this, Nintendo most likely has them working on another platformer, and with rumors of a Yoshi game as far back as late 2011, I suspect it might be true...but it could grace either 3DS or Wii U. It has been quite a time since the last release, too.
Headstrong Games - ???
Reasoning: Just released a game, doubtful we'll see anything for a long while.
Monster Games- (shot in the dark) Wave Race [2013]
Reasoning: It will have been two years since the 3DS launch title (which was probably a little over a year in development), and Nintendo did renew the the Wave Race trademark/copyright(?) along with Eternal Darkness. Now, ED2 was being pitched by Silicon Knights, so perhaps they started with Nintendo for a short time and incited the renewal for it. Either way, something is coming from Monster Games very soon, I suspect.
Next Level Games - Luigi's Mansion: Dark Moon [Spring 2013]
Reasoning: Obvious, of course. Doubtful they are working on another project.
Skip - ???
Reasoning: Are they still alive? I suspect so, but they are fairly small in scale. Hard to see what they could be making at this point.
Vanpool - Second Dillon Game 3DS [2013?]
Reasoning: There seems to be some level of hinting that a sequel could be made, and I would not rule it out, either, as just about all of Nintendo's DD games on 3DS did fairly well and got sequels of sorts.
Platinum Games - Anarchy Reigns (US/EU) (pub: Sega) [2013], Metal Gear Rising: Revengeance (pub: Konami) [2013], The Wonderful 101 [2013], Bayonetta 2 [Late 2013/4]
Reasoning: Three major releases all announced, probably out by 2013 (with possible 2014 release for B2).
Knowing this, my Nintendo-focused anticipations of 2013:
3DS
Brain Age: Concentration Training (SDD) [Feb]
Fire Emblem: Awakening (IS) [Feb]
Pokemon Mystery Dungeon (Chunsoft) [Mar]
Luigi's Mansion: Dark Moon (SPD, EAD 1?, SPD 3) [Mar-Apr]
Animal Crossing: New Leaf (EAD 2) [Q2-Q3]
Jam with the Band (SDD) [Summer-Fall]
Wave Race (Monster Games) [Fall]
Alpha Dream Project [Fall-Winter]
3DS Legend of Zelda (EAD 3) [Holiday]
3DSWare
Tokyo Crash Mobs (Mitchell) [Jan]
HarmoKnight (GameFreak) [Mar]
The Denpa Men 2 (Genius Sonority) [Q2-Q3]
Dillion's Second Adventure (Vanpool) [Mid-to-Late 2013]
Wii U
LEGO City Undercover (TT Fusion) [Jan]
Game & Wario (SPD 1 / IS) [Feb-Mar]
Wii Fit U (EAD 5) [Feb-Mar]
Pikmin 2 (EAD 4) [Apr-May]
The Wonderful 101 (Platinum) [Spring-Summer]
EAD Tokyo Project (probably 3D Mario) [Holiday]
Retro Studios Project (New IP?) [Holiday]
Wii Sports U [Fall-Winter]
Yoshi's Land [Winter-2014]
Monolith Soft Project (JPN-only) [Fall-Winter]
Bayonetta 2 (Platinum) [Winter or into 2014]
Wii U Ware
Panorama View [Spring]
Google Maps [Spring]
Virtual Console [Late Spring-Late Summer]