I actually have major connection problems with my AirPods. It's been happening since day one and I've been trying to trace down the problem.
This website describes my problem basically exactly as I'm running a 6S with a paired Apple Watch. I unpaired my watch today and ran with no issues for over an hour, but as soon as I paired my watch again the audio and pairing issues returned. I need my Apple Watch paired more than I need my AirPods to work, but it's still unfortunate. The AirPods work flawlessly when I'm using them with my MacBook Air as well as my iPad. The issue seems to reside in the phone somewhere.