I've been a Star Wars fan for almost as long as there has been a Star Wars to like, and yet I find myself strangely at odds with the majority of Star Wars fans for one simple reason: I really, really liked The Phantom Menace. I'm not going to say that it's my favorite of the films (I won't rule out the possibility), but in all seriousness, it's the one that I enjoy watching and re-watching the most.
The prequel trilogy benefits from the fact that all three films were conceived as a complete thematic unit a priori, and not merely ad hoc. There is more there for the interested viewer to latch onto. A great deal of the antipathy towards the prequel trilogy among fans may stem from the fact that the movies are far denser, in terms of both visual and thematic content, than any of their predecessors. This is understandable, considering that these early films carry the heavy burden of establishing context - building a world - for everything that follows. In doing so he has managed the sly trick of recontextualizing everything we thought we understood about Episodes IV-VI - revamping them without revoking them. To a group of fans who regard the original trilogy as "Holy" (their word, not mine), even the slightest recontextualization undoubtedly feels like a knife in the back.
As much as I love Star Wars, it has often been hard for me to defend the movies on the basis of their not-so-subtle ideological content, the exact same themes on which much of the excessive philosophizing has been built. At their core, the original three movies propose an almost Medieval value system, a world of blind animistic obeisance to unseen forces and unwavering commitment to spiritual asceticism. It's hard to rationalize this subtext in a post-Enlightenment world. Not surprisingly, Christian evangelicals have always responded strongly to coded messages of piety and submission in the films, despite the frequent Buddhist overtones that also sneak their way into Yoda's pronouncements.
To my mind, the single most significant and gratifying element of the prequel trilogy was the creation of the Midichlorians. The fans weeped and wailed that the Force had been reduced to such a literal and mechanistic plot device, but this one revelation totally redeemed the movies in my mind. Whereas before the films had portrayed the Force as a kind of universal "Holy Spirit", an invisible manifestion of the Godhead in the presence of the faithful (and wicked), the conception that the ability to tap into the Force is merely the function of microscopic parasites is ingenious. It irrevocably changed every facet of Star Wars mythology, adding layers of complexity where before there had been none.
The primary theme of the prequel trilogy is corruption. Power corrupts, almost inexorably. The Force is not a blessing, it is a blind and insensate power that scars all those who use it. Those who embrace the "Dark Side" - the villainous Sith who embrace the unrestricted license which the noble Jedi deny themselves - are corrupted by the use of the power, just as the Jedi are corrupted by their pride and the Draconian self-abnegating measures they institute to prevent the abuse of their power. I don't think it's a coincidence that the two most powerful characters in the Star Wars universe are also the two most wizened and bent - Yoda and (Emperor) Palpatine. The Force has used them, the Midichlorians operating as parasitic symbiotes to consume the host bodies. Sure, they may seem spry and athletic in the prequels, leaping and running and whirling through the pixelated air, but all their magical power also renders them strangely impotent. They are vulnerable to the pervasive doom of their destiny, fastened to the pre-Christian notion of "doom" as an irrevocable compact with fate. The more power you have, the less free you are. In the Star Wars universe, God is a powerful idea, but it is also, ultimately, chimerical - too potent for mere mortals to harness without being burnt and broken - a sobering idea for those Christian ideologues who embrace Lucas' stories as their own. In a wonderful bit of anti-theistic repudiation, Darth Vader was revealed to be a virgin birth - but not a child of divinity, but the product of ruthless genetic design, a vessel for power through untrammeled ambition.
This undoubtedly came as a harsh bromide to anyone who grew up with an image of the Jedi as kind and incorruptible symbols of chivalrous honor. But throughout the prequels, the Jedi were portrayed as arrogant, superstitious and tragically unyielding. Episode III states in no uncertain terms that the Jedi fail because they have become bloated and unfocused, with Yoda's once-insoluble wisdom rendered strangely soggy by the mad rush of tragedy. Throughout the course of these movies - some twenty years - we saw them unable to identify the "Phantom Menace" in their midst, unable to see the delicate machinations of their foes, unwilling to look past a blind obedience to prophecy in order to grasp the concrete nature of the very real dangers surrounding them. Of course, their prophecies would eventually be fulfilled, but only in the nasty way that most self-fulfilling prophecies have a way of coming to fruition: yes, Anakin would eventually bring "balance to the Force", but only after he's become Space Hitler and killed many billions of people.
Whenever prophecy rears it's ugly head in popular fiction, my eyes roll - there is no less modern an idea than predestination. The existence of free will is absolutely mandatory for any conception of individual determination in a liberal society. Thankfully, the notions of prophecy and predestination have been roundly debunked in the prequels, as the Jedi's dependence on superstition and hollow ritual to the expense of common sense play an enormous role in their downfall. The image of Yoda in Episodes V-VI has changed from wise and righteous to chastened and defeated - sadder but infinitely wiser. There is far more pathos - and much more dramatic potential, for those raised with the image of Yoda as the apogee of oracular greatness - in seeing a righteous man overcome by hubris than in seeing him fall through no fault of his own. It's the stuff of tragedy since the very beginning of drama, and it still resounds, even when the vehicle is a two-foot tall green Muppet. Even an eight year old, watching The Revenge of the Sith, should be able to tell that Yoda and his cohorts screwed up: infallibility is a myth.