There were plenty of real elements used in the PT, Lucas just doesn't want to admit it, so all the "making of" stuff focuses on the digital work. There's a convention I go to every year and for several years one of the guests was Carol Bauman from ILM. She showed workshop pics of ILM crew working on models of Coruscant buildings and various craft from TPM and AOTC (ROTS was still in production at the time).

Various digital FX animators, ILM and otherwise, have all gone on record as saying that natural elements - water, smoke, fire, rock formations, etc. - still take a lot of work to generate in CG and look convincing, so they have to resort to the old ways for those elements, at least for now.