I had a thought while watching RLM's AotC review:
Basically I agreed with his sentiment in TPM that there was no main character- but I thought AotC would not be guilty of this (surely Anakin is the main character!). Sure! It has two main story threads: 1. Anakin and Padme go on a picnic, fall in love, and kill some Tusken Raider babies and 2. Obi-Wan chases down a lead to who might be trying to kill Padame, finds some clones, and starts the war which leads to the "dark times" he is so fond of...
But how different is this than ESB? 1. Luke goes to train with Yoda for a bit until he decides to rescue his friends and teach Vader what he gets when he messes with the Skywalker family and 2. Han and Leia are on the run from Imperials, hiding out in asteroid fields and mining cities in the clouds, fall in love, and eventually get caught by said imperials (and taught what they get when they mess with the Skywalker family).
Who is the main character of ESB? Luke, of course. But Han & Leia are also main characters... but Luke is certainly the mainiest of characters.
So why doesn't the same hold true of AotC? As far as I can tell, it really comes down to this: The Plot. The Plot of Attack of the Clones is about... the Clones... Attacking. This Plot is the "action" of the piece. And it's about Obi-Wan. Anakin and Pandame are in the "romantic sub-plot", like Han and Leia are in ESB.
Since a romantic subplot is required for the Prequels to make any sense (assuming Star Wars babies are made in the same way as xhonzi's babies) it's tempting to put Anakin and P* on this romantic subplot for a whole film. Since Star Wars films by nature are small ensemble pieces, it makes it really easy to say, "While A and P are off falling in love, the other plot (the action!) can be handled by Obi-Wan (& Bail (& Owen (& Red Lid'r (& Young Han Solo)). Note: Most other action movies do not have this problem. Indiana Jones and James Bond can handle falling in love AND kicking bad guy butt and solving the mystery/saving the day AT THE SAME TIME!
I guess it comes down to this: Obi-Wan (and company) will feel like a 5th wheel if they're hanging around the whole time Anakin and NotPadme are trying to fall in love. Getting them off on their own romantic adventure seems like a priority... So what do you do with everyone else? Why not send them on an adventure!
So, if you can solve this little proble: Give Anakin the major plot action and some alone time with Notpadme so they can fall in love- I think you will have solved the major problem of the middle part of the NPT.