Thank you for your post. In my experience with the many 2016 servers I have in my lab, patching is considerably a bit slower than the rest of the OS's I patch which include the ones you've mentioned. A lot of this I feel has to do with the size of the updates that are put out. For example, this current month's full CU update is 1.17GB. Any patch that I have seen over 200MB can take an extended amount of time just for the sheer size of that patch. Now I have seen that when you can use the delta versions of those patches, it doesn't take quite as long, but is still going to be longer in general than other OS's.
I would agree that this seems to be something with the OS and possibly also related to how Microsoft is packaging the updates. I'd be interested to hear if anyone else experiences this as well.
We are also seeing slow patching on Windows Server 2016 and have been since we deployed it several months ago. For us an hour would be a short install time for a 2016 servers, we've been seeing 1 to 3 hours just for the CU. It happens whether deployed with Shavlik or through Windows update so i'm not sure this is a Shavlik issue.
When we first deployed 2016 I thought it was just us as I couldn't find any other people complaining of slow patch time. I still think there must be something wrong with our server config or environment. I feel like if everyone was experiencing these slow patches more people would be talking about it. For now we've just been adjusting our patch window to accommodate the long patch time.