When you're discussing what is best about the Prequel Trilogy, I think it's a cheat to cite John Williams' score or the special effects, simply because they're not unique to the prequels. Asking whether Williams or ILM did an excellent job on any Star Wars project is like asking if the movies were in color; it's a given.
Now, if we look at elements unique to the prequels, that leaves us with...
- Ewan McGregor. It's not easy to replace one of the greatest actors of all time, but McGregor definitely succeeded. He completely sells his performances in each part of the trilogy, progressing from apprentice to journeyman to master with confidence and authenticity. I'd gladly watch more Obi-Wan solo adventures if McGregor starred in them.
- The Order 66 montage. The emotional lynchpin of the PT. Shot after shot of Jedi being betrayed and murdered by their own troops, backed by Williams' epic score... to me, it make the whole PT worth it. Powerful, bravura filmmaking.