PROBLEM:
The management of maximised windows in Unity is principally flawed and could potentially cause confusion.
This problem arises due to the location of the toolbars of maximised windows, and the global menu in the Unity panel.
Consider the screenshot at
http://cdn.omgubuntu.co.uk/wp-content/uploads/2011/07/2011-07-19-150134_1366x768_scrot-1.png. In the screenshot, you can see that because of the dark theming of the toolbar of the image preview window, it appears to be a part of the panel and the global menu.
The screenshot demonstrates a situation in which this is undesirable. It may appear to the user that the toolbar for the image preview application is a part of the global menu for the settings application. A similar problem may arise in the event that a user has, for instance, two documents open in a word processor, and one maximised behind another unmaximised window. In this case, it may appear that the toolbar of the window behind operates on the window in front. This could cause confusion and annoyance.
SOLUTIONS:
There are a number of potential solutions, including theming inactive windows differently and displaying the title bar of full screen windows.
In my opinion, the best solution I have observed is the solution in use on Mac OS X Lion. Lion creates a dynamic workspace for each maximised window, in effect treating maximised (or full-screen) applications as additional workspaces. This means that it is impossible to end up with a situation where an unmaximised window is in front of a maximised window.