Best RPG with Xenoblade, best 3rd person shooter with Vanquish, best 3D character action with Bayonetta, best 2D fighting game with KOF XIII, best 3D fighting game with VF5, best 2D platformer with NSMBU, best 3D platformer with Mario Galaxy, best shmup with Mushihime-sama Futari. Also lots of random offbeat stuff like Tokyo Jungle, Resonance of Fate, Catherine, Every Extend Extra, Valkyrie Chronicles, 999. Of course my taste in games is RPGs/platformers/fighting/shmup and I don't really care for FPS games, sandbox games, MMOs, RTS games, western RPGs or dungeon crawlers. Genres which are primary the domain of western devs.
Of course Japan is hurting in mindshare in the west, but that's because of false narratives being pushed by the western games press, a lack of faith in products from Japanese devs and their localization team (when was the last time you saw a non RE/non FF/non Nintendo Japanese game get TV commercials in the US or euroland?), a marketplace where handheld gaming dominates (in contrast to the west where nobody takes handheld gaming seriously), and a new more casual batch of game players coming in who are more interested in facebook farming games or (on the total opposite end) COD/Halo and nothing but COD/Halo... who won't be adventurous enough to pick up that obscure Japanese (or obscure Western) IP... people who in the past would have broadened their horizons and picked up something out of their comfort zone not being able to, due to the bad economy.
Square? Bravely Default and Type 0 are both reported to be excellent. The DQ7 remake is pretty ambitious considering the original is one of the longest games ever made and is now getting a total graphical overhaul. DQX was also quite a hit for the company. But unfortunately their localization sucks lately. Also FFXIII-2 wasn't half bad either.
Nintendo, in shambles? Well, the Wii-U may not being selling up to expectations but I would hardly call it being in shambles (Sony is doing FAR worse).
Namco makes plenty of games but a lot are anime adaptations that don't come out in Japan. But this gen has been pretty good for US Tales fans, and those games are generally pretty good. They also published both Dark Souls and Ni No Kuni, and released Tekken Tag 2 which is an awesome fighter oozing with content (and I'm generally not a Tekken guy).
Konami, no argument there
Hopefully Ground Zeroes will be good.
Sega, they started off pretty strong with the Platinum deal, but their focus on going digital-only kinda sucks. Even though we got a fully-translated Monster World IV out of them, which is fucking amazing.