It's probably not what you think, but it's not great news for people who prefer to root their phones.
As anyone who roots their Android phone will tell you, it's not always easy to play the games you love these days. Lots of game developers deploy anti-root detection methods to keep you from playing their game if you root your phone. An all too common explanation for why this anti-root philosophy exists is to combat cheating, and one place in particular this explanation irritates users is Pokémon Go.
Niantic won't even let the app fully start if it looks like you are rooting your phone, and the method being used to look for whether your phone has root access rubs a lot of people the wrong way.
Stay out of my file system
In order to tell whether your phone has root access, Pokémon Go on Android asks for permission to look at your file system. This is a fairly common permission for an app to ask for, since most apps need to write something to your phone, it's not a huge surprise. But in a recent update to the app, that permission access is being used to look for files and folders which are commonly used with root apps.
Niantic is being very aggressive about how it is looking for these things and deciding if you're cheating.
This is messy for two reasons. First, it's kind of not cool for an app to be poking around in your folders without telling you it is doing so. Even if you have given the app permission to read your files, there's nothing about the way most people use Pokémon Go that suggests it is going to behave this way.
Second, and perhaps more important, Niantic is being very aggressive about how it is looking for these things and deciding if you're cheating. It's not uncommon for someone to move data from one phone to another when upgrading, which means all it takes is a folder labelled with a name like a root app for Pokémon Go to completely shut you out until the folder is removed.
This clearly isn't a big deal to a lot of people, given how few folks actually root their phones these days, but creating this much inconvenience for users who either do currently root or used to root at some point, especially with zero communication to the user, sucks.
No harm in explaining what you are doing
The sad truth is, there are folks who use root access to fake their GPS location and mess with the way Pokémon Go is supposed to be played. This gives those players an unfair advantage, allowing them to play from their living room when everyone else is running around town. And while location spoofing is the most common form of cheating, it's not the only kind. Manipulating the game for your own benefit ruins the experience for everyone else, and Niantic is right to deploy mechanisms to combat these people for the benefit of the greater community of players.
Is it likely Niantic will reverse this policy? No.
But it's clear some of these methods are going to extremes, especially when coupled with a lack of communication in the app. There's no dialogue to explain why the app isn't letting you play because that makes it easier for the actual cheaters to build a workaround. Niantic is in a stick position, because every person who would never use root access to cheat is being punished. And again, just having an empty folder related to root apps is enough to make this security "feature" kick in.
Is it likely Niantic will reverse this policy? No. Unfortunately there are way more people out there who complain about cheaters ruining the game on a daily basis, and Niantic is going to appeal to the larger audience every time. And while there are ways around this existing problem for people who root, the dance between exploit and patch is going to continue for as long as these companies see benefit in stopping even a couple of cheaters.