Note: No solution available, pending Apple TV software update per Netflix.
If I had to guess, it was around early to mid November when the shows that we normally watch on our Apple TV 3 (in Netflix) started, buffered for a very quick second, played in great quality for about 20 seconds, then dropped to what seems to be well below DVD quality. We have 35mbps down via Comcast as measured by speedtest.net and tried everything there was to try to get the quality better. Of course, nothing worked.
So yesterday, I gave it one more push. We tried using Netflix on our SmartTV but it wasn't the greatest and we tried it on our PS3 which seemed to be normal HD (1080p-ish). I read about certain cable companies throttling the SuperHD streams from Netflix. I then called Netflix and before I could finish my sentence, the rep knew what I was trying to say. He confirmed that the latest version of the Apple TV doesn't properly decode the video stream and that the Netflix engineers are working with Apple's engineers to get that fixed in the next update.
...here's hoping that's soon.
Hope this helps anyone else that has been fighting this issue. You're not alone. ;-)