The problem with your argument is that this is an administrative GUI that isn't even normally presented to end users unless you search for it or know how MMC snap-ins work. It is a power-user interface by all measure.
And while Microsoft does simplify UIs for end users, they don't typically do the same for administrative content (just look at anything in the Admin Tools, or MMC snap-ins, no sugar coating there).
Your argument about backwards compatibility is at best confusing. What does the data stores utilised have to do with UI representations of the same? I can name numerous examples where things changed behind the scenes and the UI was just updated to support it (e.g. Disk Manager now supports ESP, and exFat, same UI, ConHost now supports Powershell, same UI, Defrag now supports Trim for SSDs, same UI, etc).
> So yeah there are two or more places where certificates are stored. Typical users only care about the abstraction of web security so that's what Windows surfaces.
No, it doesn't. As the blogpost clearly shows it doesn't "surface" all root CAs usable by websites.
> Application developers should choose the new store for new applications. Existing applications can use the old method.
Huh? What do application developers have to do with this? I don't see the connection. This isn't talking about the custom root CAs you may install, it is talking about Microsoft's list of preinstalled ones.
> System administrators and security consultants should make themselves familiar with all the documentation and double their rates.
Please link to the documentation about this on Microsoft's site.
> Bloggers, however, are still free to write linkbait headlines using the Windows bashing meme.
Aside from the word "lying" (which is emotive), the title is largely accurate. Windows does mislead about installed trusted root CAs. And nothing you've said in this apologist answer has come close to addressing that, you're just dancing around it.