Neither of these are Apple's doing - obviously in the case of "Microsoft User Data", and I don't know what "My Music" is but Apple's software puts music in ~/Music. (Heh, it seems I have a "My Music" in Documents, as well as "My Documents", "My Pictures", "My Games"… not sure whether this is Wine or VMware's doing, or whether they're there for the same reason as on your system.)
Applications are not supposed to use random subdirectories of Documents (that's what Library/Application Support is for), and in the case of sandboxed Mac App Store apps, can't. But I don't know what you want Apple to do about random unsandboxed third party apps deciding to do it anyway. I guess if the Mac App Store had been more of a success, more apps would be sandboxed, but still…
I guess it would be nice if macOS made it easy to sync custom (existing) folders to iCloud rather than just desktop and documents. But if you're starting from scratch, you can just create the folder under iCloud Drive and drag it to Finder favorites. If you're a CLI user, add a symlink in the home directory or whatever.
I agree iCloud Drive on iOS is really inconsistent and awkward, and it would be nice if you could share folders with other users. I don't know what you mean by "no way to share into your drive", though. You can add arbitrary files to iCloud Drive from the share menu (and you can access arbitrary files from the iCloud Drive app).
My Music etc., are made by Apple. My Music is Garage Band, I believe. My Videos would be iMovie, I believe. I think savegames end up in Documents because they are considered to be "documents" as opposed to app state (which would go under ~/Library/Application Support), but I'm not sure what the Apple guidelines are.
"Microsoft User Data" is apparently from earlier versions of Office. Newer versions will look for it in ~/Library/Preferences, and you can actually move the folder there to get rid of it. [1]
Here [2] is my Documents folder. It's 100% crap that I did not ask for.
As for sharing: This discussion was about macOS, although the same limitation applies to iOS: There's no way to share an iCloud Drive file directly. If you do right-click -> Share -> Email, you get an attachment that you need to send, even though the file is already reachable through the cloud. Every other competitor (Dropbox etc.) adds a "Copy Link" option to the Finder context menu.
The current version of GarageBand saves projects under ~/Music/GarageBand by default. and iMovie uses an opaque "iMovie Library" in ~/Movies. I'm not sure about older versions, although from a quick Google it seems unlikely to me that it used those directories.
Apple's documentation[1] implies that applications are not supposed to use the documents directory themselves (only when the user selects it in the file picker).
Neither of these are Apple's doing - obviously in the case of "Microsoft User Data", and I don't know what "My Music" is but Apple's software puts music in ~/Music. (Heh, it seems I have a "My Music" in Documents, as well as "My Documents", "My Pictures", "My Games"… not sure whether this is Wine or VMware's doing, or whether they're there for the same reason as on your system.)
Applications are not supposed to use random subdirectories of Documents (that's what Library/Application Support is for), and in the case of sandboxed Mac App Store apps, can't. But I don't know what you want Apple to do about random unsandboxed third party apps deciding to do it anyway. I guess if the Mac App Store had been more of a success, more apps would be sandboxed, but still…
I guess it would be nice if macOS made it easy to sync custom (existing) folders to iCloud rather than just desktop and documents. But if you're starting from scratch, you can just create the folder under iCloud Drive and drag it to Finder favorites. If you're a CLI user, add a symlink in the home directory or whatever.
I agree iCloud Drive on iOS is really inconsistent and awkward, and it would be nice if you could share folders with other users. I don't know what you mean by "no way to share into your drive", though. You can add arbitrary files to iCloud Drive from the share menu (and you can access arbitrary files from the iCloud Drive app).