The biggest differences between menu scenes & regular scenes are:
1. menu scenes do not have way systems
2. menu scenes have no z-index support (object centering) & the layer order is instead controlled by the order of the objects you add to the scene.
3. because menu scenes have no way systems, they do not support characters.
4. menu scenes contain the option to create save slots on them as well as the ability to specify the default mouse cursor for that particular scene.
Even though menu scenes are not really geared towards playable scenes, you can however still use them for first person close-up views of parts of your regular playable scenes &/or for first person mini games etc... well besides the typical intention of them being used to create menus.