Things I liked:
Overall: The score. John Williams did not disappoint.
Episode I:
*The visual design of Naboo. Beautiful.
*Seeing the Jedi in action. It's not as unnecessarily flashy and over-the-top as in the other prequels.
*Coruscant and the senate chamber, also stunning.
*The final light saber duel. A lot more believable and less face-palming than in the other PT duels.
Episode II:
*Coruscant again. If not for the speeder silliness, this could have been a great opportunity to explore the dark underworld of Coruscant.
*Kamino. The dark, stormy waterworld with bizarre tall aliens really added to the mystery.
*Arena scene on Geonosis (before the Jedi arrive). Also interesting and tension-filled to see how the Jedi operate with no lightsabers.
*Count Dooku. An intriguing character I wish had been explored in more depth.
Episode III:
*The opening battle. A great way to kick start the film, though it was quickly lost in the droid silliness/implausibility of the elevator escape. If you had never seen AOTC, you might actually believe Obi-wan and Anakin are friends.
*Dialogue between Anakin and Palpatine. McDiarmid really shines here.
*Anakin's fear of loss turning him to the dark side. This really makes this a classic tragedy. It could have been executed better of course. I would have liked to see the brutal nature of war play a role in his turn as well.
*The duel. I liked it well enough until all the hopping on the lava river near the end.
*Yoda/Sidious duel. I hated most of it, but the idea of them fighting in the senate chamber was interesting. I liked the later stages when they were fighting mostly with throwing pods and lightning. After all, Yoda had to do something about Palpatine, and it was nice to see that.
*The closing scenes. I enjoyed finally seeing Alderaan. Seeing Palpatine and Vader overlooking the Death Star was spine-chilling the first time I saw it. Delivering Luke on Tatooine really tied up the film nicely.