I'm also having this issue, iPhone 6S+, Apple Watch 2, Airpods.
Resetting the iPhone is, I think, useless... I had just activated a new 6S+ and did a clean setup, no restores from backups and very few Apps installed.
In my experience unpairing the Airpods from the iPhone, then repairing them results in a period of them working as expected. Usually until I don't use them for a while, like overnight.
After a while they will never connect to the Watch, unless I put the Watch briefly in Airplane mode. Afterwards everything works fine again for a while.
MBP (15" late 2013) also has problems sometimes switching to them. Have to manually connect them almost every time.
In a call, using both pods will disconnect after about 20-30 mins into the call.
Ironically, connecting them normally as a Bluetooth device to a MS Surface worked perfectly. This gives me hope the issue is software related to how W1 handles the handoff.