My biggest problem with AOTC is the editing, which I always found troubling, since Lucas' background is that of an editor. The Anakin-Dooku fight needs a LOT of work to make it as smooth and clean as the other saber fights are in the film.
The Geonosis arena sequence stands up as awesome today, in my opinion, and the "recycled music" doesn't bother me so much, since there was a lot of music from the ANH end battle that was - not duplicated but very close - used in the ROTJ end battle.
Going back to some of the animatics and stills, I miss some of the shots and material that wasn't included, like clonetroopers shooting Geonosians out of the sky, and the short sequence where Dooku is fighting with two sabers. I would really have liked to see those two things in the final film. The exclusion of those short bits relates back to editing. Some of the compositing work in that movie could use improving also. I hope to see that on the blu-ray release.
I am probably one of the few who appreciates Hayden's performance in AOTC. I immediately and permanently identified with where his character was during the fireplace scene. Who among us hasn't been that 19-year-old guy, pouring hs heart out to the unattainable girl, only to have her react in the most uninspiring way possible?
This is the only film in the series where my opinion is slightly influenced by the public's perception of the film. Since this movie came under so much heavy criticism (some of it justified), I tend to emphasize the good things I like in this movie as opposed to the other films. There is so much good stuff crammed into this movie, it remains as enjoyable for me to watch as any of the other five films.