First of all, and I'm sure I'm not alone in this, I love John Williams' musical scores in the SW films, and in the majority of his non-SW work. Even his low-key scores, such as the one for "A.I.", are absolutely incredible and carry as much emotion as the on-screen action, and any fan of SW (or movie music in general) should have his scores in their CD collection.
I absolutely adore the RCA Victor releases of the Special Edition soundtracks: two discs for each film, in sequential order, with all kinds of bonus tracks, unreleased cues, and unsurpassed liner notes. Those three double-disc sets are among my most loved SW items in my collection and I listen to them on a regular basis. Sure, they weren't as complete as they could have been ("Lapti Nek", the Yub Yub song, and the Rebo Band source music from just after the Boussh thermal detonator scene aren't included), but they are an absolute treasure to fans of the films.
That said, I have been less than thrilled with the presentations of TPM and AOTC on CD thus far. Not only have tracks been slapped together that have little or no relation, not even thematically, some of the most memorable cues from the films have been ignored completely (such as Anakin's breakdown in AOTC with the soaring Sith theme blending into the Imperial March). I do enjoy the soundtracks a good bit, as there are some incredible pieces of music on there, but compared to the RCA Victor releases of the OT:SE, they come up way short.
(I will say that one thing I love about the AOTC CD is that it does include a lot of music that wasn't in the film, mainly during the Speeder Chase and the Arena Monster Battle.)
Sony tried very poorly to follow up on the OT:SE work with a TPM "Ultimate Edition" that was marketed to make people believe it was along the lines of the SE soundtracks. When it was released, people quickly realized that it was nothing more than an isolated score, and still featured the choppy editing and abrupt transitions that plagued Williams' score in the film. People, myself included, were outraged, as Sony had led people to believe it would be one thing, were intentionally vague when asked questions about specifics, and once it was released, tried to cover up by saying "we never said it was all that was recorded, just that it was "every note from the film." Thank goodness they didn't give AOTC a similar treatment, as the music editing in that film was 10 times as worse as TPM's.
Now, I know the reasons for the score in TPM, particularly during the four-prong final battle, being as choppy as it is due to Lucas reediting the final reel after JW had done the score. And I know that in AOTC, Williams didn't even score a lot of the Clone War because he knew it was not finished and his work would probably wind up like TPM's. But what I don't get, with all the money Lucas has at his disposal, is why Williams isn't given the chance to rescore both TPM and AOTC's endings so the music won't sound like a temp track. Give him and the LSO some extra money to stay around for a week after the recording session for Episode III (or come in for another session ala Howard Shore for the LOTR:EE DVDs) and let things be set right.
After that, let RCA Victor have the rights to all the soundtracks and let them release two-CD complete scores of all three prequels the right way. For all Lucas goes on about sound being so important and how much he loves John Williams' work, he has really torn it apart with the prequels and it'd be great to hear things as JW intended them to sound.