Maybe John Williams was daunted by the task of making cose to 6 hours or whtever of music.
But yeah, Samuel Walters I'd love to hear about it because I'm one of those that knows close to nothing about music (other than I know I like this or that kind of thing) but would be open to hearing the flaws in the prequel trilogy's score.
I'll start by saying that, for me at least, the score of a film is something I truly enjoy and pay attention to, but by no means am I an expert in music or composition -- I'm just an enthusiast. Also, I actually like the Prequel trilogy (warts and all), but the score for AOTC remains one of my biggest disappointments.
Part of the issue with the score to
Attack of the Clones is probably from Williams himself. That year he also had film scores to
Chamber of Secrets, Minority Report, and
Catch Me If You Can. I'm guessing that, purely because of workload, AOTC wasn't at the same level as either TPM or ROTS. But, I suspect, the score would be much, much better if it wasn't for the way Lucas made the film.
The real problem is that Lucas didn't actually have a completed film until long after Williams composed and recorded the score. Simply put, Williams didn't have a full film to work with, which is probably why the score is bland -- at least by Star Wars standards. And, I think this is why so much tracked (re-used) music is in the film.
In any case, the entire Battle of Geonosis, from the moment Mace Windu appears up to the lightsaber duel between Dooku and Anakin and Obi-Wan, uses music that was recorded for
The Phantom Menace. You'll hear clips from the Battle of Naboo, and even the opening scene when Obi-Wan and Qui-Gon are battling droids on the Trade Federation ship. I still don't know why they didn't have Williams at least record some source music that they could have used for the battle.
I also think there was a missed opportunity to make use of the Stormtrooper Theme from
A New Hope. It's the music you hear on the Death Star and was replaced by the Imperial March in
Empire. Making use of that theme (giving it a slightly different variation, say) for the clones would have been a masterstroke. And would have given Williams a pair of themes to utilize for source music for the Geonosis battle (heck, even the bloody Ewoks have their own theme). But I honestly don't think the powers-that-be were thinking about musical themes for this movie.
What's even more tragic is that a bit of what Williams did score doesn't even end up in the film. There's a whole segment from the Arena (when Anakin, Padme and Obi-Wan are fighting the monsters) that isn't used (inexplicably it does show up in ROTS, though). And there was a piece for the droid foundry that wasn't used (or barely used) because Lucas re-edited the sequence.
Listening to sound and film editor Ben Burtt's commentaries and interviews, I think part of the blame can be placed on him and his love of sound effects and editing -- I think his efforts marginalized Williams' work.