This is an otherwise amazing game but it keeps being marred by this experience. I don't understand how every other game can simply work and detect a gamepad and this masterpiece works only some of the time.

It's very frustrating. I've installed the 360 emulator and tried every solution only for it to stop working when I boot the game up again. It's very annoying. What makes Witcher 2 so special that the controller works every time without any BS. How is this still a problem years after the games release? Why doesn't a permanent fix exist? Why does it feel like a dice roll everytime I start the game to see if the controller works?

Exactly what kind of 360 emulator are you using? Witcher 3 doesn't require anything special, just like in the Witcher 2 a wired or wirelss Xbox 360 gamepad works out of the box. Maybe your problems are related to using software you don't need for this game.