Lucas has himself admitted that
Phantom Menace was a disappointment, with McGregor chiming in to a similar effect. I personally think the pacing is a bit awry and there's far too much Tatooine. That's before you factor in any lovable Gungans!
However, I think it does do some things right.
It portrays the Jedi order in their prime. We can see that they were once well schooled in philosophy and combat and that they keep close council on those they enrol.
Coruscant looks fantastic.
The senate and all the political talk is dry, but I think this helps. The more Anakin and others are incensed by quibbling beaurocracy, the more inclined the viewer is to agree. From the first episode we're looking foreward to the end of democracy -- to Episode III.
Anakin is at this stage totally innocent. In fact he's downtrodden and chipper inspite of it. "Yipee!" and "Are you an angel?" might have been ill-advised lines or perhaps performed better but there's no doubt that Anakin is free from the dark designs of the force here.
Qui Gon Jinn is the coolest Jedi ever.
The Prophecy that one will bring balance to the Force. It echoes common tenets in common religions ie. second comings, judgements, the afterlife etc. More importantly it makes clear that all 6 films are about Anakin Skywalker, his life, his legacy, his family.
Palpatine's plan is already well under way by the time the film starts. His story preceeds the prequels, the true measure of his genius is not fully revealed to the protagonists until he decides to do so. Just like the set up to Return of the Jedi.
Attack of the Clones starts where Phantom Menace left off. With Palpatine watching Anakin's career with great interest. From the beginning of the movie you learn Anakin has become a great pilot, skilled warrior... and a good friend. But you also learn he now has troubles. Anxieties. Fear. Fear leads to yadda yadda yadda remember? Gone is the Anakin that races amazingly in PodRace events, and flies his way through battle & victory on the whim of a fluke. He is replaced by an awkward, arrogant and emotional person about to be derailed by the events in his life. His life being chosen, he being subject of that virgance in the force, means he can fortell the death of his mother. He is powerless to stop it. And his rage is becoming unconcealable. Fear is fast becoming hate. And someone is watching his career, waiting for the right time to use him to their advantage, in order to change the face of the whole galaxy.
Well this is where I think the whole point of these movies lies. Can your emotions and anxieties lead you to do awful things? Can you set out to do what you believe is right and instead do great wrongs? Can others corrupt you? Can they eclipse the good in you? If they do, is that good gone forever, or can you still redeem yourself and your love? Can loved ones learn from your errors? Can they help you to be the person you should be? Make you act in honor and pull you from the depths of darkness & disapair?
These films may be more obviously hammy than their Old Trilogy counterparts, but they weren't completely ham-free themselves. These are expensive takes on sci-fi B movies. They're inspired by flash gordon, spaghetti westerns and samurai movies. And people seem to expect writings on a Tolkien level. They're just fun adventure movies that carry universal mythological themes, and boast awesome lightsabre battles and effects. Anyone can watch them. That the first three made had such charasmatic stars as Ford, Fisher, and the voice of J.E.Jones are just fortunate truths that the first two Prequels couldn't possibly have hoped for.
Nobody else makes anything like these films. To some, they might well be crap. But it happens to be something I really love watching. I'm glad Lucas pursues things his way.