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I think there are many better layouts of debugger windows than the current. A user usually needs to see as many 'important' information in one view as possible. But he/she should not be overwhelmed by many opened windows. IMO at least Breakpoints, Call stack, Watches and Local variables views should be 'always' visible. In the other hand Projects, Files, Navigator, Favorites or Runtime windows can be minimized and toolbars like UI gestures, Profiler and maybe Build or File can be disabled.
Created attachment 40045 [details] example
You could use the perspective plugin to create such a window layout. http://plugins.netbeans.org/plugin/3273/perspective