for me, AOTC is two movies. others have mentioned the groanworthy love story sequences, and I think they suck hardcore. yet there's also this interesting little mystery flick where Obi-Wan becomes an intergalactic gumshoe to track down the mystery of the dart and the Kaminoans and the clones.
what fails miserably is that this mystery is pissed away by a) Yoda basically shrugging and flying off to Kamino to pick up an army THAT THEY DON'T EVEN KNOW WHO ORDERED IT OR WHY, and b) absolutely NO follow-up on who deleted the planet from the Jedi Archives and who Sifo-Dyas was.
(and I get that the info may be in the books, and maybe we're supposed to assume Dooku or Sidious was behind it--but SPELL IT OUT, GEORGE. we're the audience. there are things we like to know, such as the particulars of a freaking story we've paid ten dollars to watch.)
my edit would cut the love story down to the bone and use whatever means possible to expand the mystery stuff--i know AOTC was the only prequel with a co-writer, and my honest theory (supported by nothing but my brain) is that Lucas penned the love sequences, told Jonathan Hales to leave them alone, and Hales largely penned (or at least, heavily influenced) the Obi-Wan sequences. cause to me, it's like two different movies.
but yeah--cutting the pauses, the stiltedness of the whole affair, the wasteful sweeping establishing shots and transitions would help a ton too.