Gurm Nobody has found anything definitive that they can turn off and go "HA! IT WORKED!" so we're sort of stuck.
Well, we can narrow it down to something to do with the way the OS renders content to the screen. The OS alone shouldn't affect refresh rate or flicker. It can affect dithering and color. Unless the driver subsystem was changed, that could do it to
Kray If this theory is true, that means if we install apps that changes the color profile of the phone like CF.lumen, then there might be a chance that the app will override or eliminate whatever it is that is causing the eye strain in the new OS.
That was me. Unfortunately those "color filters" don't change the way the dispaly render colors. It just changes the color it is displaying. For example, if you are sensitive to particular spectrum of blue light the display emits, f.lux and the like won't change that from being emitted. It will just add red and green to the color display to make it look less blue.
ICC profiles work by actually changing the way the display shows colors. Unfortunately Google has decided not to add ICC support to Android, which is weird since there already exists an ICC profile class for Java so it would be trivial for it to be incorporated into the OS, and color accuracy is a huge deal for photographers and have kept smartphone from really being considered high end cameras, but they have handwaved away the issue like so many people who do not suffer our symptoms. You can search the Android bug report/suggestion forums for ICC and see the discussions.
Kray Can someone give this a try?
I did already. I have a Moto G, zero issues with a Skinomi screen protector and Lollipop, massive eye pain when it was upgraded to Marshmellow. I tried every light filter app out there, changed screen protectors, adjusted every display setting, nothing worked. Ultimately I had to restore the phone to stock and root it to block the update.
Kray We take one theory or possible solution at a time, and try it out, and see if it works or not. And hopefully one of the theory or possible solution actually works.
Yeah, I know I keep harping on it, but honestly, the color theory is the only theory that actually would explain every instance of eye strain I have experienced from any device and/or lighting source.