The Base design is useful when you want to share templates along different designs. If you have a template that you use in two or more designs, you can put it in the Base design instead of copy-paste it in the two directories. In the siteaccess/site.ini.append.php you can see that Base design is configured as a <i>additional design</i>. This mean that if a template does not exist in the actual design, eZ publish will try to find it in the Base design before it search in the Standard design.
You say well, but after getting feedback from EZ Crew I will add that the BASE DESIGN and THEMES is a layer of EZP customization to be offered out the box, approaching a completed portal solution out of the box
To me is the EZP approach to deliver out of the box solutions, similar to phpnuke and the likes
