1. Seek out skilled and passionate independent development studios throughout the world. Make offers, beginning with single-game funding offers, with expectation that those studios that live up to expectation can expect offers of purchase, or failing that, ongoing contracts for more games.
2. Contact Warren Spector and organise for him to join Retro Studios. Have Retro Studios form into two distinct "teams", one focused on the more colourful titles (a la Epic Mickey, DKCR, etc), while the other focuses more on the darker types of games (a la Metroid), with Warren Spector given leadership of the 'colourful' team, and Retro employees expected to migrate between teams as demands fluctuate. At any one point, have one team working on an existing franchise (of their choice) and the other working on a new one, alternating which team is working on a new IP.
3. Arrange deeper partnerships with Sega and Ubisoft, with an eye to possible merger with the former and formalised second party status with the latter. Crossover games with these companies, and with other companies (Capcom, Namco, Activision, Square Enix, and Marvelous/Natsume) would be arranged, perhaps on a rotating schedule if agreements can be reached in which Nintendo develops one crossover with one company's game, while another company develops another crossover (so you might get a Sega-developed Metroid+Alien Syndrome while Nintendo develops a Harvest Moon x Animal Crossing game in one year).
4. Modify the approach to the Wii Sports brand, by creating a kind of two-tier arrangement - free versions of games featuring the kinds of features found in the original game along with online functionality (basically, the Wii Sports Club stuff, but without any cost to play), with deeper and more realistic versions of each sport to become available for purchase in the future. Try to get big names to headline the more realistic versions (Tiger Woods for Golf would be great). "If you liked Wii Sports Club Golf, you'll love Tiger Woods' Golf!"
5. Expand the Wii Fit line of games to be a more generalised brand. Include more "serious" games that are designed to make use of the same sorts of control schemes found in the Wii Fit games already. First "serious" game to come with the Wii Fit branding? Super Mario, with Obstacle Course elements along with real Mario type gameplay.
6. When it comes to Mario's main games, I'd look at changing up the way they're approached. I'd have 2D games released yearly, downloadable, with additional content available if you buy more than one of them - I'd also have a Wii U bundle and a 3DS bundle that lets you get them for free as they release. I'd have 3D Mario of the "3D World" variety released every 3 years (per platform), with "Galaxy" style Mario released the following year and then a spinoff style Mario on the third year.
7. Zelda would be placed on a similar arrangement, but with a release every two years. New Zeldas would be expected to release every 6 years, with a spinoff Zelda from the same engine two years after that, and then a third-party spin on Zelda two years after that (the idea being that the third party would work with the engine created for the first one, but structure the game differently, etc). Obviously, the third-party one would be under strict Nintendo scrutiny during development, but it could mix the franchise up a bit more. Handheld Zeldas would fill the gap years.
8. Minor "core" franchises would be placed on a five year rotating schedule - that is, it would be expected that Star Fox, Kid Icarus, F-Zero, Metroid, and Pikmin would take turns, each year, being released. A similar arrangement would be made with the other comparable franchises. On a side note, Sakamoto would no longer be permitted to do anything with the Metroid series - however, give him freedom to create a new franchise.
9. On the off years for the Zelda team (that is, when the third-party variation of Zelda is being made), the Zelda team would be tasked with developing a completely new IP. Similarly, those behind the various Mario titles would be expected to create a new IP every 3 years (between them). The goal would be to have at least one new IP every year, with two to three when possible, across the entire company, not counting games developed by independent studios with Nintendo funding.
10. I would have Miyamoto given two roles - Quality Assurance, and his own studio. His studio would be given complete creative freedom. In his other role, he would be expected to, with the support of a dedicated team, playtest or concept-test various games throughout the company. His dedicated QA team would be trained in identification of issues, and in the Miyamoto style of addressing them. This would operate separately from the normal QA process used by Nintendo.
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