God, that Yoda/Dooku duel was so terrible. The original trilogy established Yoda as this Jedi who was so powerful he didn't even need a lightsaber, then the prequels shit all over it by having him hop around ridiculously and swinging around an adorable mini-lightsaber.
Also, I thought the third movie looked awful too. It was just another CGI shitfest where Lucas tried to throw everything imaginable on the screen. It was a mess visually. That last lightsaber battle was a fucking joke. It was utterly ridiculous, silly, and lacked any real emotion, mostly because both Obi-Wan and Anakin had the charisma of a particularly dull block of wood, and the movies didn't spend any time giving them any actual characterization.
The best lightsaber fight in Star Wars is easily one of the two duels between Luke and Vader. My personal favorite is the second one in Return, because that's the one where Luke snaps and just starts hammering Vader. There's more emotion in that fight alone than in the entire prequel trilogy, and that's what made the original trilogy fucking good.
Someone told me yesterday that Lucas had an interview recently where he said that Disney shot down every idea he had for the new trilogy. If true, that gives me hope that it might actually be good. I also question how much of the original trilogy was great because of other people shooting down Lucas' terrible ideas.
tl;dr I'm honestly not sure which of the prequels was the worst. I generally lean toward the third one because I fucking hated every moment of Star Wars by that point, but they're just all do goddamn bad.