I am speaking off the cuff as someone heavily involved and interested in RF in general and WiFi/LTE in particular.
From my anecdota(shame this isnt a word), Atheros chips have better SNR and higher symbol discrimination thanks to cleaner amps, better signal discrimination logic, and tend to be on the forefront of newer RF techniques in the WiFi space. All this culminates in better throughput, latency, and spectrum utilization than anyone else.
It also helps that their support under Linux is far superior to most everything else, which helps in Router/AP/Client integration and testing.
I don't even like Qualcomm, but from my experience, you will almost always regret choosing someone else for anything but the most basic requirements.
A big frustration with Qualcomm wifi on Windows has been that they do not provide driver downloads to end users. If you are using a laptop that has been abandoned by the OEM and you have a wifi driver problem you have to hunt for the driver on sketchy 3rd party sites or just live with it. I have personally had to help several people find drivers because ancient Qualcomm drivers were causing bug checks on power state transitions.
What real-world experiences have you had with Intel wifi on Linux and Windows that make you believe it is second rate?