Re: The Win 32 API has huge significance.
Sadly, many of those "flaws" are exactly what makes Windows applications usable. The clipboard needs to be shared, or how do you exchange data across applications?
Sending messages and input to different processes is subject to User Interface Privilege Isolation since Vista.
Processes that "syntehtize" keyboard and mouse inputs are useful 1) to assist people with disabilities 2) virtual keyboards 3) automated testing applications (even X has support for that). Anyway you need the proper rights to achieve it.
Desktops *are* "securable objects" (see https://msdn.microsoft.com/en-us/library/windows/desktop/aa379557(v=vs.85).aspx) just most application would stop working properly if secure desktops were used, because a lot of "Windows" developers learned coding for 3.1/95 and have no clue about Windows security. Even most password input boxes could be eliminated if developers had learned to use Windows AD and how to integrate their applications in its security model.
Raw access to the "desktop" happens in browsers as well - where injecting code you can easily overlay what you like over the "real" site - clickjacking & C, anyone? Sure, get rid of the GUI and you're much safer, restrict system to only one application running like in DOS and you're even safer...