For instance, I see some advantages and disadvantages of the 3D method:
Advantages:
Can use AnimatorControllers to give excellent effects like fade-ins and fade-outs
Can do more advanced things, such as radial controls, easier than with the built-in GUI system
Can incorporate 3D models into the GUI if you wish
Can give perspective, shadows, etc. very easily
Disadvantages:
Scripting becomes slightly messy, as either each control needs to have its own script to control its behaviour, or a very monolithic controller class with handles to each of its controls has to be written.
Dynamic lists, which could easily be handled by ScrollViews become a little more tricky