Hi folks,
I'm having the same issue like many described before me but here's one more thing.
Since iOS 10.1 I'm having a lot of trouble with my iPhone 6s connection to the handsfree system in my car (Audi A6 2016). The bluetooth connection is dropping again and again, especially during phone calls. Most of the time I can reconnect but then it's dropping shortly after. No iOS update since then has changed that.
Few times (since iOS 10.1) I've had other bluetooth headphones dropping as well. But it happened not so frequently. I already thought I've had a hardware issue with my car's system.
Since a couple weeks now I'm owning my AirPods and the problem appeared there as well.
Like the most of you I also have an AppleWatch (1st gen.) paired to my phone.
I believe we're seeing a general bluetooth problem rather than an isolated issue with the AirPods & iPhone 6s combo. I hope the attention because of the AirPods will help the issue being surfaced and fixed.
BTW: If I'm putting my watch on AirPlane mode a couple minutes before I get into my car, most of the time it's working stable again. Thanks a lot for this tip!!