You know, I have to say that Wedge has an amazing take on these films. I had never thought of the story mechanics that lay behind Jar Jar and the Gungans, and after reading Wedge's posts, I can appreciate that their presence in the script was in some ways a far more subtle piece of work than we tend to give Lucas credit for. Further, in terms of how all the pieces fit together across the entire span of the six films, it may well be that TPM tells the most vital information and has the heavy responsibility of grounding the entire series, which is a difficult task. It may also be possible that the overall story-telling was handled as deftly as it could have been, and I can see the argument for an unfair maligning of Lucas' work on it. Kudos Wedge, I love reading your ideas here. Definitely food for thought.
However, I think that my view of the film ultimately has to be heavily colored by how much I actually enjoyed watching it... and sadly it just wasn't that much. No matter how cleverly the script was constructed or how brilliant the allegory was, it ends up falling a bit flat if you can't stand to watch the actors performing the lines, or if you can't stay awake through the entire 12 hour pod race sequence. In some ways I consider TPM a bit of a minor tragedy, because the underlying story is actually such a good one. I find it unfortunate that Lucas didn't have a Lawrence Kasdan around to punch up his screenplay or an Irvin Kershner to get something more out of the actors. With better performances and less focus on the CGI elements, I think the film really could have been something special. Unfortunately, it ended up instead as one of only two SW films where I actually have to skip certain scenes in order to get through a viewing. The story Lucas wanted to tell seems like it really was a worthy one, but his efforts were severely undercut by some of the most wooden acting I've ever seen, and- in the case of the Gungans and Anakin- some pretty flat characterization that left me feeling absolutely no emotional attachment to either, which makes the whole venture a much harder sell. Jake Lloyd's performance forces me to dislike Anakin's character at a point in the films when he's supposed to be at his most likable, and Jar Jar and the Gungans are such overt cartoon caricatures that I can't help being embarrassed for them every time they're on screen.
Having grown with the original films, it's possible that I just have a bias that I can't overcome- but it really does feel to me like the potential that was inherent in TPM from its inception was just not cultivated or capitalized on in a way that could be made real for audiences. As a result, the film received a fairly negative reception from a lot of quarters, probably from a lot of people who- like myself- sensed the film's unrealized potential, and lamented its unsatisfying final cut.
But, I know a lot of people really do love the film as well, so... horses for courses. :)