Linux isn't perfect, but neither is Windows. For each exception raised for Linux, I'm sure I can find one for Windows. Let's not go down that path or we'll be here all night.
There are a few points that need clarification, though:
- Do all Windows-based applications use Windows Automatic Update? No. There are many disparate update systems, and some involve downloading large files and re-installing. Some updates can conflict with each other.
- Do Windows users stay with one version forever? No. Even service packs can have significant effects and 'break' applications. There are some Long Term Support linux distros and upgrade options exist for many between those LTS (and other) releases. E.g. CentOS has a 7-year life cycle.
- The CLI is not required to install packages from a distro's repository or any other participating/partner repository (which, for the uninitiated, is a collection of programs on the web you can install from). Setting up repositories doesn't require the CLI either. The great majority of applications are provided in a distro's own repo or partner repo, so you don't need to go wandering off to find something you need. Of course, as with Windows, there will be exceptions to the rule.
- I've not yet had a package (i.e. program) that required only KDE or Gnome as the Desktop Environment. If you want to install, say, Kaffeine media player in Gnome, just go ahead - it will install the dependencies and it looks Ok to me. But why do that anyway - if you're so hooked on KDE apps, use a KDE desktop. Otherwise Gnome has it's own default apps. But again, nothing stopping you from selecting what you want. And having multiple sets of apps/libraries installed (which don't conflict, BTW) is still less space-hungry than a typical Windows system (apps included). Why is this choice a 'bad' thing? Choice is good!
- Skype is available in the correct installable format for seven major distros (and their derivatives) from the Skype website right now (including Debian).
Most of the improvements you say are needed for Linux aren't even available for Windows. Since when did all Windows applications include updated device drivers? Ever had an error and fixed it by separately updating the driver - direct from the vendor? This occurs frequently in Windows. And modifying repos to enable auto updates? This is the default situation in Linux, where the distro's (or partner) repo is used - which is already the case for the vast majority of software installed by Linux users. To repeat - does installing an app in Windows cause Windows Automatic Updates to include it? No, of course not.
Linux is a lot better than you make out, and I think it's a bit misleading to say that, to be usable, Linux must include improvements that Windows doesn't, and for the foreseeable future won't, have.