AirPods choppy/unreliable when connected to Mac, but not iPhone Problem
In my apartment, when using the AirPods with my Mac, the audio is significantly choppy, fluttery and unreliable. There are frequently small &quot;pops&quot; when listening to music. The issue is not present when using the AirPods with my iPhone.
The Apple Stack Exchange question you are reading now, is actually an update to my question on the same topic that was posted and resolved here previously. I had this very same issue while on macOS Sierra 10.12.4. We found out that the culprit was a bug introduced in that particular macOS version, and the problem went away with 10.12.5.
I am now on 10.12.6 and having a quite identical problem. But I'm not confident that the OS is at fault this time.
The reason is that I recently swapped my AirPods for a new pair, via an unrelated Apple support ticket. The new ones arrived via mail and I was instructed to pair them with my original case.
The new pair of AirPods seem significantly more prone to skipping, stuttering and losing connection. I did not have this problem with my original AirPods, which I also used with 10.12.6 without problems (at least that I am cognizant of).
Possible explanation
I think I have found what's causing the skipping (albeit not the root cause), and it seems to be my iPhone Bluetooth signalling with its environment. Whenever that happens, there is a glitch/pop on the Mac ←→ AirPod connection. When I disable Bluetooth on the iPhone, the problems go away.
I haven't changed anything in my environment except swapping the AirPods. No microwave in the background etc.
I am quite confident that the reason is Bluetooth interaction from the iPhone. I am just not sure how to proceed, because the weird thing is that the problems started just when I replaced the AirPods for a new pair.
Some plausible root causes are:

The new AirPods are in fact defect or come from a batch that are not as 'good' with Bluetooth.
macOS 10.12.6 introduced a bug similar to the one in macOS 10.12.4, but I didn't realize it until much later (not that likely IMO, knowing how sensitive I am to audio quality).
The pairing process whereby new AirPod buds were paired with an original case didn't go exactly right, and there is a firmware or software problem somewhere.

What I have tried

'Hard Reset' of the AirPods according to these instructions;
Resetting the iPhone Network Settings after &quot;Forgetting this device&quot; (the AirPods) as part of the AirPod 'Hard Reset'.
Resetting the Mac Bluetooth Module according to these instructions.
I solved this choppy audio issue with just one simple trick.
(This might not work for everyone, but I solved it this way)

Short answer

If your hardware uses Bluetooth 4.0 instead of 4.2 or above, this solution is highly likely to work for you.

Open System Preferences > Sound > Input

Change sound input from Airpods to Internal Microphone

Long answer (+ Possible explanation)

(This is just my hypothesis based on my observation)

First of all, to clarify my symptoms,
I am using a MacBook Pro 15 inch (Late 2013) which has Bluetooth 4.0 hardware.
The choppy audio issue only happened in my MacBook Pro, and it did not happen in my other Apple devices such as my iPhone 7 Plus (which btw, has Bluetooth 4.2), nor my iPad Pro (also Bluetooth 4.2). 

Based on these observations, my hypothesis is that Bluetooth 4.0 devices have too low bandwidth to handle both input/output (microphone &amp; speaker) at a high quality. However, if I just change the audio input to the internal microphone, the Bluetooth connection only delivers sound output, so I think it can handle higher quality audio. On the other hand, if I use both microphone &amp; speaker on a Bluetooth 4.0 device, I think the connection degrades and sacrifices audio output bandwidth in order to make room for delivering audio input.

Indeed, according to some sources, Bluetooth 4.2 is 250% faster and has 10x more capacity

Reference:


https://www.quora.com/What-are-the-main-differences-between-Bluetooth-4-0-4-1-and-4-2-in-the-Layers-Baseband-LMP-L2CAP-app-Layer
https://www.semiconductorstore.com/blog/2015/BLE-4-2-vs-BLE-4-1/1548/