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Forcing users to use keyboard-mouse pair to navigate through desktop could been painful. People like to use mouse, but using mouse in some cases could be painful, because most DE are development to being use with keyboard and mouse (for example - I can play full screen game or hide panel with task manager).

Solution: develop mode, which allow to fully use DE only with mouse. User could switch between normal mode and mouse focused. You can use similar techniques like in tabled mode, but it will be designed to use mouse in mind.

For example:
1. When mouse only mode is enabled, pressing right-mouse-button and next left-mouse-button will allow to do default alternate action with window under cursor.
2. When long press right-mouse-button menu with possible actions will appear:
a) When right-click on item menu, user will set is as default-alternate-action for window management
b) When left-click on item menu, action will be executed

Suggested actions:
a) Submenu - menu of current window
b) Submenu - window list
c) Submenu - list of most used menu options of each running windows on current activity
d) Resize window
e) Move window
f) Hide window
g) Move window behind
h) Move window above
i) Submenu - select different activity
j) Submenu - select different desktop

To avoid long press of right-mouse-button being handled as mouse-window-management menu, allow to click on right button and user could now long press right button - it will be delivered to app.

In my opinion, it only in small amount made usage of some app harder. But we can try to avoid this by:
1. Disable mouse - only - mode on windows, which grab mouse
2. Allow to switch menu activator (long right-mouse-button press) to long press and shake mouse cursor.