You make some excellent points. However, any form of digital communications can be the victim of misuse. SMS is often misused but can be incredibly effective. Email marketing is often misused but can be incredibly effective. I also agree that NFC and VR will become very popular, but they are not there yet.
If you plan, test and test some more, you can effectively integrate QR Codes into your communication strategy. And integrating them into visual design strategies can be done quite well as you can see in the McDonalds example posted in the comments above.
I believe that QR Codes will continue to be effective for those companies who are using them well.