If you haven't heard, Nintendo is preventing rooted Android users from using Miitomo by running a check at launch, and killing the app if root access is detected. There's a workaround, but it requires Xposed, which itself is too "hackish" for my liking on a daily driver.
I'm more than a little miffed that I can't use the app on any of my devices, which all are either rooted or running custom ROMs - mainly to get rid of carrier bloatware, run newer Android versions, and give me the ability to actually tether. Definitely nothing that I think Nintendo is worried about happening to Miitomo.
But more to the point, it's increasingly obvious that Nintendo will block root users in all future titles as well. They're the only company I know that has been consistent about this. (See: Pokémon Shuffle and Pokémon Jukebox. Ninty may not have developed those, but they are the parent company ...)
I mostly love Nintendo and their software, but I'm not giving up greater ownership of my devices just to walk with them on their journey into the smartphone age.
EDIT: Version 1.1.2 presumably reduced the strictness of the root check, as Miitomo now runs on my main phone without issues. I've heard reports that it still won't work for many Cyanogenmod users, so that's a bummer. I'm using Miitomo now, and it's neat, but it's probably not worth the trouble of removing root/reflashing stock/flashing Xposed just for this one (battery-eating, while in the foreground) app.
