GDI had so many bases who were important. Sure, the Philadelphia was the biggest and most important base. But the pentagon, seen here above, Hammerfast with their sonic and ion technology, Goddard Space Center in Maryland, Manchester with a major GDI headquarters, Andrews Airforce Base on the east coast of America- and so are there probably enough locations.
GDI and NOD have their important bases everywhere. It's not like they all have 1 base in 1 region that will be the heart of the organisation.
NOD's Sarajevo Temple, NOD Cairo Temple, Command Center Ayers Rock in Australia, Vega's Temple in South America, Hassans Temple in North Africa, Cabals Core in Cairo- you can continue.