Have read through fairly quickly, so might have missed it, but I haven't seen any mention of Silverlight!
Yes - that really is a reason we keep getting people calling and saying "Please install Silverlight because I need it for <crappy website>". They get nowhere trying to open the site in Edge.
The second most common issue is that people find PDFs opening in Edge. Mostly they prefer Acrobat Reader DC or whatever other tools they have installed.
The third is that they do not have necessary print options when printing from Edge.
The fourth is using Remote Desktop (or has that recently changed?) which has always needed IE to work easily and reliably.
And my hate, unable to use it in a domain admin account. It isn't that I want to use it, but I have to positively change defaults in order to avoid things trying to open in Edge.
Finally, the fact that time after time, portal.office.com (yes, the 365 portal) fails to open pages time after time. The tab just stays blank and requires one or more F5/refreshes before it will appear. Works far better in FireFox.