Something that annoys me with the current multi window system in 2.79 is that if you close the main window the child windows stays open and if you decide to save at that point then next time you start the scene you end up with only the child window, the main one is forever lost. Would be nice if they can fix that behaviour so that when you try to close the main window Blender will either ask if you want to save, or in case it is saved already, just close all child windows with it.
There are 3 major, really frustrating issues with Blender’s multi-window support right now.
When main Blender window is restored from the taskbar, child windows are not restored and focused with it.
When closing main Blender window, child windows remain open instead of being closed with parent window, resulting in you having still opened instances of Blender which you have intended to close.
Child windows show as a multiple entries on windows taskbar, instead of single one.
The little change that has been done in 2.8 to introduce concept of child windows does not solve any of these 3 issues, which are critical for the proper multi window support. I hope eventually all of these will be resolved, otherwise this would be very sadly missed opportunity.