In AOTC I thought the story was worse, the script was worse, the directing was worse...I still can't stand the Dexter's Diner scene, Jango is stupid, Mace has the worst lines of the saga (Even worse than Jar Jar), the tracked TPM music was infuriating, the Arena concept is just plain gay, the CGI was irritating (mainly the clonetroopers and bad looking sunset at the end made it look like a cartoon), the love story is impossible to buy, the supposed mystery was solved in 5 minutes when Padme suspects Count Dooku, the duel was extremely short...and I think Yoda went over the top...the icing on the cake was the Death Star subplot...it just pissed me off because why would it take twenty plus years to build when the second one, which is bigger takes only four??? Don't even get me started on Shmi staying alive for a convenient MONTH just so she could die in Anakin's arms....HORRIBLE.
Finally...it seemed Lucas did away with the midichlorian thing....something I wanted to see pan out instead of just hanging there.
One constant between the two was that the humor is just stupid and infantile...especially the fecal jokes and Threepio droid factory subplot (Which has the worst CGI in the saga, btw...)
Sorry didn't mean to rant.