Just FYI, I posted this topic at TF.N, as well.
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First off, let me just point out that I've been away from these forums for a considerable amount of time, so I apologize if this topic has already been discussed. Also, as noted in the thread title, this post contains major spoilers for those who have not yet read James Luceno's "Darth Plagueis" novel, so be warned.
Now, let me clarify that I very much enjoy the prequels. However, I feel that in a perfect world, Lucas would have sat down and planned out the events of the entire PT at the outset of writing "TPM". It's painfully obvious that most of what he came up with after "TPM" was on the fly. By this, I mean that many of the trilogy's more intriguing elements and plot points (Sifo-Dyas, Dooku) are either short-changed or left entirely unresolved. I think it's safe to say that had Lucas conceived the entire PT from the beginning, most of these subplots would have been given the justice they deserve.
On the one hand, I kind of enjoy that "TPM" possesses this sort of disconnect with the other prequels; it takes place a full decade before the second film in the trilogy, there's no real political intrigue beyond Palpatine's ascension to Chancellor and the bad guys (excluding Sidious) all lose in the end. Much like "ANH", it kind of exists in its own bubble and could potentially work as a standalone film. On the other hand, even though I cherish "TPM" for what it is, I know that for the good of the entire trilogy, the Clone Wars should have begun at some point in that film to set the stage for the rest of the trilogy. Obviously, with the Original Trilogy, the sky was the limit, since there were no preconceived notions as to what had to happen to the characters. Lucas could have kept Darth Vader alive as long as he wanted and kept creating new adventures, new characters etc. but he wisely, in my opinion, decided to wrap up the story in three films.
Enter Luceno's "Plagueis" novel. What stood out to me most about this book is the rich backstory it provides for many of the events of "TPM", as well as the entire clone army mystery from "AOTC" which it unravels in superb detail. I don't think anyone can argue that had Lucas established the clone army conspiracy, characters like Darth Plagueis, Sifo-Dyas, Jedi Master Dooku, etc. and Darth Plagueis' "experiments" before writing "TPM", they would have all played much larger roles in the first two films, if not in "ROTS", as well.
I've always felt that the character of Count Dooku is one of the greatest missed opportunities of the PT. I would have loved for Christopher Lee to appear in all three films; Dooku and Qui-Gon Jinn were obviously kindred spirits in many ways, and it would've been a treat to see Lee and Liam Neeson interacting on-screen. There are a few scenes in "Plagueis" in which Dooku expresses his disillusionment with the Republic and his thoughts on Anakin and the Prophecy; these types of scenes could have gone a long way towards planting the seeds of Dooku's fall to the Dark Side between "TPM" and "AOTC". (And don't get me started on how ridiculous it is that the Lost 20 scene was cut from "AOTC").
Then there's the subject of Sifo-Dyas and the mystery of who deleted Kamino from the Jedi Archives. Originally, Sifo-Dyas was called Sido-Dyas, a pseudonym Palpatine/Sidious used to place the order for the clones and subsequently peg it on the Jedi. However, it was, I believe, nothing more than a typing error that resulted in the inception of "Sifo-Dyas" as an actual Jedi Master, yet this character neither appears on screen in any of the films, nor is he mentioned again after "AOTC".
I suppose it could be argued that the issue wasn't important enough to dedicate any screen time to in "ROTS", since it's obvious that it was either Sifo-Dyas or Dooku who did it, but I would have liked some actual confirmation. Am I the only one who feels it was incredibly reckless oversight on Lucas' part to completely abandon this storyline in "ROTS", especially considering it was one of the driving forces of "AOTC"? Come to think of it, the mystery could have been resolved as early as the end of "AOTC". Dooku could have given a conclusive answer during his duel with Obi-Wan, at which point he could have also dropped the bombshell that it was he who murdered Sifo-Dyas. The film would then end with the Jedi in possession of the unsettling knowledge that not only was Sifo-Dyas killed by a former Jedi-turned Sith, but that it was one of their own who essentially thrust the Republic, and in turn the Jedi, into the war. On top of all this, could the Jedi even see fit to divulge this information to the Senate? What would the Jedi accomplish by revealing that one of their own went behind their backs and placed the order for the clones? It would be a PR nightmare. It would be the ultimate catch-22.
Last, but certainly not least, there is the subject of Hego Damask/Darth Plagueis. Short of performing a drastic rewrite of the "TPM" script, there's probably no way to really develop the Plagueis character a great deal without turning "TPM" into a three-hour movie. However, I think incorporating him into just a few key scenes would make a drastic difference. One way to accomplish this is by having him as part of Palpatine's senatorial entourage on Coruscant. I picture his presence being similar to Lobot's in "ESB" in that he'd be this somewhat creepy character who doesn't appear to do or say much but is always present when his employer/friend is on screen. I don't think I'd even make it clear that Plagueis is a Sith (he would never be referred to by his "Darth" title); however, I would definitely retain the fabled scene from the novel in which Palpatine kills his master.
There's the argument that showing Senator Palpatine doing "Sithly" deeds (including, as I mentioned above, killing Plagueis) in "TPM" would destroy the mystery of his duel identity prior to the 'big reveal' in "ROTS". Now, I saw "TPM" in theaters when I was eleven, and not once did the possibility cross my mind that Palpatine and Darth Sidious could be two different people. I cringe at the thought of some of the "Palpatine/Sidious is a clone" theories that were bandied about before the release of "ROTS". I suppose the only actual drama that could be had by trying to preserve Palpatine's hidden identity would be for first-time viewers who are watching the films in chronological order. My point is, I'd rather forfeit the so-called "mystery" of Palpatine's alter ego in favor of some more exposition and insight into Palpatine's machinations.
Below I've described a few key scenes I would campaign for to be included in a hypothetical "TPM" rewrite. Were I a talented enough writer, I would attempt this myself; perhaps one of you budding writers is up to the challenge? 
* The death of King Veruna - In this scene, Plagueis infiltrates Veruna's hidden castle in the Western Reaches of Naboo and murders him by essentially disassembling his midi-chlorians. Ideally, this would be done without it being made obvious that Plagueis is a Sith Lord, as I wouldn't want to blow the lid on Demask's secret identity so early in the film. This scene would put the film's primary plot into motion as Veruna's death leads to the Trade Federation's attempted invasion of Naboo. It would also serve to bring to light the corruption that runs rampant on Naboo and would explain how and why Padme Amidala became Queen at such a young age.
* Demask's proposition to Sifo-Dyas - Unfortunately I do not currently have the book at my disposal to go into greater detail, but for those who have read it, some iteration of the scene that has Demask at a gathering with Sifo-Dyas, suggesting to the beleaguered Jedi that he seek out the cloners on Kamino and place an order for a human army to defend the Republic.
* Sidious and Maul - The scene wherein Sidious and Maul converse on Coruscant would be the exact same as it is in the film, except that the scene would end with Plagueis spying on them from a distance through macrobinoculars, his concern over his apprentice's growing relationship with Darth Maul visibly apparent.
* The death of Darth Plagueis - Obviously I don't really need to describe this, as Palpatine himself does so in "ROTS". I picture a much more toned-down iteration of the scene from the novel. I'm not sure where in the narrative of the film it would slot in, though, as the novel mentions that Plageuis' death occurs almost simultaneously with Maul's.
* Palpatine courts Dooku - The death of Qui-Gon should be the final straw for Dooku's decision to leave the Jedi Order. This scene, which occurs at the end of the "Plagueis" novel, sees Palpatine and Dooku at The Works on Coruscant, with Dooku voicing his disenchantment with the Republic and declaring his decision to leave the Jedi Order.
I know there are probably several other noteworthy scenes from the novel about which I'm currently forgetting. Now, I'm curious--What are your ideas?
