Steam’s big picture does a lot to remediate some of the challenges of working with a controller in a desktop environment. The ROG Ally additionally has switchable modes between desktop and gamepad and it allows for mouse movement with the thumbsticks and stuff in addition to the touch screen.
It also has this app called Armory Crate SE which is basically an Asus-branded game launcher like GeForce Experience where you can fine tune settings on each game.