Other than the things I've been clamouring for since day one, like a fully featured activity log, from my experience with Zelda—and specifically, taking over 600 screenshots with the Capture button in Zelda—I want to see more photo uploading options that aren't tied to social networks (though adding a wider selection of third-party networks/sites would be a welcome alternative). I want to share screenshots on the web as easily and non-intrusively as I did using Miiverse or Imgur (through the browser) on the Wii U, and I don't want to pollute the social media accounts that I do want to link to my Nintendo account for future friend-finding purposes.
The leanness of the OS doesn't bother me otherwise, since it's clearly built for easy multitasking without interruption of communications or play (as I tested in the Splatoon Testfire earlier today; you can mess around in the OS at your leisure while waiting in a match lobby). But a musical identity for services like the eShop, even a rotating one like on the Wii U, would be grand. And eShop search/navigation will need a revision very soon as the software library expands, though I think that can probably handled entirely on the server side. I would expect menu music to eventually make its way into premium OS themes anyway, if the 3DS is any precedent.
The sooner we hear about save data backup/transfer, the better, but the Wii U never delivered a proper solution to this either.
Oh, and one more thing: motion pointing for onscreen keyboard entry.
