The company has issued a press release notifying outsiders that alongside naming a new president in Tatsumi Kimishima, the company is undergoing a "large scale revision of the organizational structure" that would take effect on September 16th, 2015.
Previously, at the commencement of 2014, Satoru Iwata began the initial wave of the second major restructuring during his reign, which created the "Business Development Division" and "Development Administration & Support Division". Iwata also officially unified the Integrated Research & Development Division (console designers) with the Research & Engineering Department (hand held designers). Additionally, there was an unofficial unification of the Entertainment Analysis & Development Division and Software Planning & Development Division, who for the first time ever began developing internal games together. Lastly, Iwata continued strengthening the System Development Division, with his protege Shinya Takahashi.
With Iwata unable to see the final reorganization through, here is the end result with Kimishima, Takeda, and Miyamoto finalizing the new internal structure.
President Iwata, Restructure, Phase 1, 2013-2015
System Development Division est. 2013 (OS development, app development, network development, casual game development)
Business Development Division est. 2014 (Development and coordination of QoL Products)
Integrated Research & Development Division and Research & Engineering Department merged in 2014. Console and hand held engineers working together for first time.
Kyoto Development Center constructed. Houses over 1500 personnel, third Kyoto building.
Nintendo Network Service Database Inc. est. Network services.
Nintendo European Research & Development est. Technology development.
Entertainment Analysis & Development Division and Software Planning & Development Division, separate entities, but sharing staff for several internal projects.
Development Administration & Support Division est. 2013. The parent of “General Support Group” which coordinates a network of small developers that provide assistance in specific departments of large scale production groups. (debugging, programming, art assets, animation, cg movies, etc.)
President Kimishima, Restructure, Phase 2, 2015President Iwata, Restructure, Phase 1 2013-2015
Entertainment Analysis & Development Division and Software Planning & Development Division merger under Entertainment Planning & Development Division
Integreated Research & Development Division and System Development Division merge under Platform Technology Development Division
Miyamoto vacating position as EAD manager, Takeda vacating position as IRD manager, taking bigger roles in the company direction. Also probably preparing for retirement.
Business Development Division is very much intact. Absorbed some staff from other hardware and non-gaming divisions.
More information to come
-- New Development Structure --—
Entertainment Planning & Development Division - Development of software for dedicated game machines and mobile.
General Manager: Shinya Takahashi
Deputy Manager: Katsuya Eguchi (Kyoto)
Deputy Manager: Yoshiaki Koizumi (Tokyo)
Platform Technology Development Division - Development of hardware, OS, network, and technology tools.
General Manager: Ko Shiota
Deputy Manager: Takeshi Shimeda
Development Administration & Support Division - Management of external contract employees? Management of external first-party games?
General Manager: Shinya Takahashi
Deputy Manager: Keizo Kato
Business Development Division - Development of QoL and non-gaming consumer products.
General Manager: Yusuke Beppu
-- Speculated Game Development Structure --—
EPD Production Group No. 1 - Hideki Konno
Mario Kart / Nintendogs series
EPD Production Group No. 2 - Hisashi Nogami
Splatoon / Wii Sports / Animal Crossing
EPD Production Group No. 3 - Eiji Aonuma
The Legend of Zelda
EPD Production Group No. 4 - Hiroyuki Kimura
Super Mario Maker / New Super Mario Bros. / Big Brain Academy / Pikmin
EPD Production Group No. 5 - Tadashi Sugiyama
Wii Fit / Star Fox / Steel Diver
EPD Production Group No. 6 - Ryutaro Takahashi
Tomodachi Collection / 2D Metroid / Rhythm Heaven
EPD Production Group No. 7 - Goro Abe
EPD Production Group No. 8 / 1 (Tokyo) - Takao Shimizu
Super Mario 3D? Flipnote Studio?
EPD Production Group No. 9 / 2 (Tokyo) - Koichi Hayashida
Super Mario 3D? NES Remix 3?
Lastly I would guess the other SPD Producers like Yamagami and Tanabe maybe have a more External Group as a denomination? Also probably Tezuka and Sakamoto are new executive officers that oversee all general things like the Deputy Managers.