When I have multiple windows open in one app, it is harder than it should be to switch between them. If one window is covering the other, I have to move it out of the way which is annoying. Otherwise I have to use alt-tab or Super+W which is more tedious than it has to be. The most intuitive way to do this is to switch the windows of the focused application when the application icon in the launcher is clicked, however that feature is absent. I have a similar problem when using OS X.
If the application has multiple windows and the application icon is clicked, it should do a "window spread" similar to Ubuntu. Then, if the application icon is clicked a second time, the windows should minimize like normal.
This would be a very useful feature, and the fact that it is absent is one reason I will probably switch back to Ubuntu from eOS.
One concept that was mentioned by ~danrabbit recently was having clicking the dock icon of a multi-window app cycle through those windows (sort of like how clicking an unfocused app focuses it).