TPM just has too much Jar Jar, and it annoys the shit out of me everytime I watch it, I just can't get past how annoying he is and how he ruins every scene. I think it comes down to this:
What annoys you more? The AOTC romance? or Jar Jar in TPM?
I can put up with the romance in AOTC, so that is probably why I rank it higher. I do like the whole Kamino sequence and the Clones, it was one of the few things from the PT that added to the OT. If you think of the saga 1-6, when Vader flies away after the Death Star has blown up, one scenario is he goes right to Kamino and tells them to get some more Stormtroopers ready, cause the Empire just lost all of them.
I guess another reason I like AOTC, is that is the only movie that ObiWan is really the lead character in the movie. Anakin/Padme are just in boring scenes falling in love, and ObiWan is really getting all the good action scenes, and he was the only character I truly cared for in the PT.
I do like the ending montage once Dooku goes to Coruscant, and John Williams score is great too, but enough about AOTC, I don't want it to come off that I actually think it is a great movie. To me it is like an election that you don't like any of the candidates, but you vote for the lesser of the two evils.