The vast majority of gamers using Windows buy their games through Steam, Origin, or other stores that Microsoft has nothing to do with. Unless we see a massive market shift then I don't see this having any affect on the future of PC gaming.
As for the game mode stuff, it's easy to turn off if you don't want it so I don't see any issue with it.
I also think that most gamers (myself included) would be okay with PC gaming becoming more consolized.
Back in the 90's you had to mess with configuration files in both the OS and the game you were playing far more than you do today. In a sense, it's because PC games have become more consolized - they "just work" most of the time. People like that. I hope the future of all forms of computing "just work" better than they do now.
I will concede that if you want absolute freedom of customization, Linux is the best OS for you even if you don't plan on gaming at all. However, saying that Linux is the future of gaming is about as accurate as all of the claims that "20XX will be the year of the Linux desktop".