MS have acknowledged recently what we have all known for ages, it is impossible to completely remove an application as if it was never there. Once an application is on the system it can do too many things completely uncontrolled for that to be possible.
They're now starting to advertise appx as the solution to this. As appx gives the application it's own hive for registry and file system, it should theoretically be a lot easier to remove an application as it's changes have been isolated.
I think they're only advertising it for UWP apps at the moment, but as the appx format came from their purchase of Softgrid, which later became AppV, I'm hoping they'll give some guidance on using it with Win32 apps as well, hopefully something that doesn't involve sequencing!
Of course, it'll take the various divisions of Microsoft another 20 years to switch from MSI to appx, so whether that will be of any help for MS applications in the short term is another question.