Layout containers help a lot with format and make it really easy to do some resize stuff but unless you put a ton of planning into your layouts before adding any visualizations it becomes difficult to add them. Furthermore, if you have to add a visualization after the fact do you really want to start back at step one and recreate a new dashboard layout again. Part of the difficulty, at least for me, stems from the fact that it is very difficult to drag a container onto a dashboard and use the gray shaded areas and blue boxes to understand where your layout container will ultimately end up. As you layer more containers it starts to feel like some containers stop showing up meaning you can work yourself into a place where you start to feel like you need to start over. I think there is an easy solution to this problem.
There is a layout pane yet beyond showing the layer containers, how they are nested and allowing some to be removed, there is not much functionality to it. What I think would be very helpful is if this layout pane could be used to drag new containers to or have the functionality to right click and create a container from the pane. This would remove the issues of trying to always drag containers to the dashboard and interpret where the container will end up. Having this type of control would allow you to know exactly where containers are being created. Another nice to have functionality, would be to use the same pane to move containers up or down a layer giving the user greater control of where content is going to be displayed.
I believe that these type changes would alleviate a lot of the frustration I, and many others, have while trying to use layout containers.