What I do like about the prequels is a pretty short list, but it does exist:

Palpatine was awesome. In an insanely over-the-top scenery devouring “EEEEEEEEVIIIIIILLLLLLLLL” way but awesome all the same. Ian McDiarmid did a glorious job and was really the only actor who looked like he was having fun. Plus the best part of the story is Palpatine manipulating his way into becoming Emperor. It’s like House of Cards meets Star Wars. This might already be a fan edit, but a movie focusing purely on that plotline could be pretty damn good. What would be even better is an alternative prequel trilogy with Palpatine as the protagonist who breaks the fourth wall like Frank Underwood in House of Cards. A man can dream.
John Williams’s score was great as always. “Duel of the Fates” is in the running for greatest Star Wars song ever.
There was quite a bit of imaginative worldbuilding and creative costume design, set design, etc. Some of it was pretty dumb, but some of it was great too. The Star Wars universe was expanded quite a bit and the effects, though horribly dated now, were groundbreaking at the time.
All the seeds for a great, Shakespearean tragedy were in place in the main plotline. It was executed terribly, but the idea was good and there were at least a couple moments in ROTS where it came close to emotional payoff. It also adds a bit to Vader’s arc in the originals, particularly ROTJ, even though at the same time the portrayal of Anakin significantly takes away from his badassery.
Ewan McGregor was the perfect choice to play young Obi-Wan. He was misused in the films (especially TPM), but this might really pay off if he gets his own spinoff film now as rumored.