I struggled with Flash on Linux for years.
I too am disappointed by the lack of desktop applications. The advent of the microcomputer has meant that we shouldn't need to connect to a server the other side of the world to do tasks - we can do 99% of them locally (unless collaboration is involved).
Whilst I agree that Windows has 20+ years of history to maintain (and it does this very well) and suffers from inconsistencies (particularly apparent in Windows 10 as they push out apps like System Settings which doesn't adhere to UI standards, I can't double-click the icon top-left to close a window like since 1990 because it doesn't exist...), I would prefer Linux did not experiment with desktop paradigms - look at the Unity and GNOME3 weirdness. It seems apparent that the normal "windows and taskbar" system has worked well for decades. You can take a Mac from the early 90s and find your way around it. Experimentation of this paradigm would be for experimentation's sake.