1. Secure all kinds of third party support for the NX.
Make the system the juggernaut it should be. We can't just rely on solely first party titles forever.
2. Increase internal storage space on the NX to far beyond Wii U levels.
In this day and age this is a necessity. To paraphrase what someone in another thread said, someone who buys most of their games physically anyway should not have to deal with storage issues or resort to an external hard drive. Make it a powerhouse.
3. Rework how amiibo are sold.
Ideally, it'd be so that certain characters would appear in certain months through a rotation, and not have certain figures never show up while the same ones clog shelves forever. I'd say the ones always in stock would be Mario, Luigi, Peach, Bowser, Yoshi (though the version of these five characters changes each month [Smash, Mario Party, etc]), Link, Pikachu, Isabelle, and the Inklings, while the remainder get very ample stock on a switch-off on a monthly or bimonthly basis. This makes availability a non-issue. In addition, new releases are spaced out more to not saturate the market too quickly.
4. Make the NX launch not suck.
Have a 3D Mario game, Metroid game, Animal Crossing game, Pikmin game, and Punch-Out!! game (I just feel it works well as a launch title). This gives some heavy hitters from the start, which all hit different demographics. Smash and Zelda would likely take a while, and as such not be launch-ready. Possibly Splatoon sequel as well. In addition, have some third party heavy hitters from this generation ported (Rise of the Tomb Raider, Bloodborne, Dark Souls, etc). Make it attractive to consumers.
5. Keep the personable element.
Nintendo, above all else, knows that customer service and fan communication is a plus. Keep this. Things like Directs and such are great.
6. The next Smash Bros. game.
Let Sakurai or whomever his successor is keep doing what they're doing. However, technically being his superior, I'd put in quite the good word for Chrom (and hopefully change his mind on him) and Henry Fleming. Abuse of power? What's that?
7. Keep making games fun.
Ultimately the most important thing, is it not? With everything that would change, let's not fix what isn't broken.