Padme was going to have a theme but Lucas said no which I think was a grave mistake. She was perhaps one of the most important characters and it would have been heartwrenching to hear her theme slowly deteriorate and be destroyed by Vaders.

At the same time... Anakin had a theme but after Episode I, I think Williams was so disenchanted with the whole project he didn't really care enough to mold it to Episode II.

Jar Jar had a theme... but his character didn't last long in the public eye.

Duel of the Fates was a good motif but was over used outside of the film, and in Episode I. It did add some cohesion.

Arguably though, the prequels had more thematic development. Williams had no intention for his themes to grow and develop in the OT because there was no plan for V or VI when he did ANH.

The Prequel Trilogy had the potential for development but I think Williams kinda... didn't care after how much his score was butchered in Episode I... and how DIFFERENT Episode II is compared to the look or feel of Episode I.

Some of it came back for III but not as much as I think ahd been intended.