Like painters have their "blue periods" and whatnot, John Williams has also his periods where his compositions sounds almost the same. I think this is the largest reason why the PT and OT music feel so incoherent to eachother.
You could compare the soundtrack of ANH (1977) with that of Superman (1978). When I was a kid, I was a fan of both soundtracks and used to hum and whistle them constantly, but I often mixed them up.
I remember in 2002, some people from TFN's music forum went to see Harry Potter and the Chamber of Secrets only to get a hint of how AOTC would sound ... and they did!
You can hear similiarities between the music during the Bounty Hunter chase through Coruscant and the music during the Quidditch match.

John Williams is not perfect in the OT either. I don't know when Luke's theme became "The Force" theme, why you hear the "Han and Leia" theme during the end of ESB when it is Luke holding his arm around Leia and why you hear a variation of Yoda's theme during the skiff battle in ROTJ.

Btw, the PT music I like the most are:
* Anakin's Theme
* The funeral theme
* The Order 66 music
* Most of all: The merging of the funeral theme with the Imperial March, in ROTS when we see the Death Star.