Obi-Wan $#&*ing Kenobi

Ewan MacGregor's performance as the younger Obi-Wan is one thing about these movies that I will defend in its entirety.  Actors have a tough time of it in Star Wars movies: George Lucas is notorious for his relative disinterest in the craft of acting and principal photography in general, being always eager to get into the editing room and see how many digital muppets he can shove into each scene.  There is really no excuse for not building a single set of Clone Trooper armor.  As if we can't tell that they just pasted Temuera Morrison's head onto a CGI body.  For these reasons, decent acting in Star Wars movies is done despite Lucas's involvement or not at all.  With the prequels, it was usually the latter. 

But Ewan MacGregor, like Harrison Ford before him, created a truly unique and likable character.  Particularly in Attack of the Clones and Revenge of the Sith, when the absence of Liam Neeson allowed him to come into his own, MacGregor portrayed Kenobi in just the way I had always imagined him to be as a younger man: wise beyond his years, unexpectedly witty, and a true badass in battle.  George Lucas once said, when telling people what to expect of the prequels, that the original Star Wars films had featured old men, untrained boys, and cripples as Jedi.  The prequels were intended to be, in part, a showcase for what Jedi were capable of at the height of their powers.  To a certain extent, he succeeded.  I'll never forget seeing Kenobi launch himself through the glass of Padme's bedroom window and onto a floating spy droid, suspended miles above the surface of Coruscant, or the ease with which he and Anakin dropped hundreds of feet through thin air to land deftly in flying speeders.  The first time I saw that I thought, now that's what a fucking Jedi should be able to do.

He was especially badass in Episode III.  It was exciting to see his old lightsaber, so familiar from A New Hope, in action before it got so battle-scarred.  And who could forget his new lightsaber stance, sword whipped back horizontally near his face, his free hand pointing a few fingers tauntingly at the enemy.  This was Obi-Wan Kenobi at his most swashbuckling, the you-don't-know-who-you're-messing-with attitude we had seen briefly in Episode II against Count Dooku and most memorably in A New Hope after he casually lopped off Ponda Baba's arm and gave the room a menacing once-over.

In all, Ewan MacGregor's Obi-Wan was a worthy successor/predecessor to Alec Guinness' memorable role.

The Lightsabers: Duels, Etc.

Seeing Luke switch on his father's lightsaber for the first time at Kenobi's place in Episode IV has got to be one of the coolest moments in science fiction, not to mention film in general.  It was cool as hell in the original theatrical version of the film, and the effects weren't even very good: the rotoscoping was done by hand directly onto the film cels.  The swordfighting in the original trilogy was epic but, as stated above, was done by old men, boys, and the handicapped and left you wanting more.  The prequels gave us that.

No matter how much you hated Episode I, I have no doubt you barely blinked throughout the final duel between Darth Maul, Obi-Wan Kenobi, and Qui-Gon Jinn and waited impatiently through the lame scenes with Jake Lloyd in the space battle above.  I bet even if you hated Darth Maul and his over the top horns and red face paint, you still thought the moment when the hangar door opens and the music swells and Natalie Portman takes one look at him standing there and says "We'll go the other way" was pretty damn cool.  I thought so.  The fight through the Naboo power plant with its inexplicable energy beams and absurd catwalks sans railings was also over the top, but in a good way.  And the final duel between Kenobi and Maul after the former sees the latter cut down his master in front of him turned Obi-Wan the simpering padawan into the quietly badass Obi-Wan we know and love.

Episode II: Attack of the Clones, perhaps the most indefensible of the prequels, had fewer good scenes.  The much-vaunted arena battle at the end of the movie was mediocre at best, the supporting cast of jedi being noticeably inept compared to the much-practiced swordsmanship of Hayden Christenson and Ewan MacGregor (though, the in-universe reasoning behind this is that supposedly that's why most of them died).  Seeing Yoda in action against Dooku was good, and a needed foundation for his badassery in Episode III.

It was Episode III that capped the general excellence of the sword fights in the prequels.  The aforementioned Obi-Wan Kenobi was uber-cool, Mace Windu finally came close to seeming as badass as he was supposed to be, and seeing Palpatine with a lightsaber put at ease those fans who thought the fact that he had never been seen to have one was a little inconsistent.

The Obi-Wan-Anakin duel was as exciting as it should have been, and yet by this point the movie-making had gotten decent enough (comparatively) that I felt more shock at Anakin's final betrayal than awe at the details of the duel itself (mostly due to Ewan MacGregor, I think). 

Yoda

The original Episode  I Yoda was a disaster.  They should have stuck with the original puppet or just gone digital earlier.  (A future release of The Phantom Menace will almost certainly include a fully-digital Yoda.)  The digital animation in Episodes I and II was pretty good, however (though not as life-like as Gollum). 

What I thought was best about Yoda in the prequels was not even seeing him fighting, but seeing him in a command scenario.  Seeing the weird little alien we know and love as a respected member of the Jedi Council and then commanding clone troops in the war was pretty cool, and like MacGregor's Kenobi, one of the ways in which the prequels succeeded as they should have.

Palpatine and The Coup

Ian McDiarmid's Chancellor/Emperor Palpatine was another great thing about the prequels, but I spend less time on him because most people, I think, would agree that he played the part well and nobody really expected him to suck.  He was as delightfully evil as ever, and seeing him slowly become the withered Sith lord we know and love was suspenseful (despite Lucas's best efforts) and cool.

One sequence that I think Lucas succeeded in, however, was the coup d'etat during which Palpatine finally seizes power overtly.  It was paced well, and included a good mix of political and military might.  Episode III was, if nothing else, an apt summation of Palpatine's amazingly complex master plan, and seeing him finally assume full control of his new empire (with the senate's happy consent, no less) satisfied me.  The duel with Mace Windu and the scene where Palpatine, now with his familiar pallid wreck of a face, first speaks with the wicked voice we first heard in Return of the Jedi was chilling.  If you think of it as the moment the Old Republic first truly becomes the Empire of the original trilogy, it is an eerie feeling.

Coruscant

Finally, although George Lucas tends to rely to his detriment on his ability to recreate any scenario with computer-generated imagery, the lush cityscape of the capitol world of Coruscant was an exception.  A planet literally entirely covered in a massive urban sprawl that stretches kilometers above the hidden surface, Coruscant could only have been realized digitally. 

The magnificent architecture of the city-world is reminiscent of Art Deco, and the sheer majesty of the towering sky scrapers and looming official buildings is the perfect setting for a galactic coup d'etat.  While Emperor Palpatine was chilling in his tower chamber above the second Death Star, seeing Chancellor Palpatine finally assume absolute power against the glowing backdrop of Coruscant at dusk in Episode III was the first time that the world of the prequels first became the world of the original movies.  The "used universe" of the original trilogy is even more evocative set against the decadent allure of the Old Republic at its height. 

These are the highlights of the prequels, for me.  There are certainly more areas in which Lucas succeeded instead of failed.  Feel free to comment and add your own.