The biggest problem with why the Prequel music may not be as good lies with--I feel--Lucas and the way he edited and re-edited (and re-edited and re-edited) those movies. Even after Williams recorded the scores the movies were changed; subsequently the scores were changed. The Phantom Menace music was butchered beyond belief-- the Ultimate Edition Soundtrack is proof of that. Plus, wasn't TPM music re-used in AOTC instead of some of the original music written for it?

I thought there were good music moments in TPM; ROTS was the best Prequel soundtrack (probably because it used so much Original Trilogy music) and AOTC did pretty much suck.