Here’s what I would have done:
Episode I sets up everything that follows in the rest of the saga. It’s a “Godfather 2” like blend of scenes that show how the rise of Palpatine in the “present” mirrors the initial rise of the Sith in the ancient past. We get to see the historical foundations of the Jedi/Sith and their conflict, in addition to beginning to set the stage for the more immediate “future” of the OT. Most of the movie would have been set in a similar-ish time to TPM (albeit not with all that crap with the Trade Federation and Naboo - basically a totally different story), but no kiddie Anakin or anything. The story instead just follows some Jedi (Obi-Wan included) as they begin to discover that the Sith might be returning. These scenes occasionally cut to scenes showing some of the ancient Jedi Order’s first conflict with the Sith. These flashbacks are short but are strategically inserted for relevance, perhaps as the Jedi research the history of the Sith. Their placement also hints at (but doesn’t explicitly reveal) that Palpatine is the Sith the Jedi are looking for in the “present.” Maybe at the end of the movie, we first see a young Anakin (who is already a padawan) in a brief cameo to set the stage for the next couple movies. Maybe show how he is selected to become Obi-Wan’s apprentice. But he is not the focus and he sure doesn’t accidentally blow up a ship.
Episode II shows, like AotC does, the beginnings of the Clone Wars and again focuses on Palpatine’s masterminding these events. However, this time give him a real reason for a war and make the stakes higher. Open the movie with a series of “false flag” terrorist attacks across the galaxy set up by Palpatine and made to look like they were carried out by an enemy (Separatists, whoever, doesn’t really matter - but don’t make the soldiers droids, make them real people). Palpatine also leaves hints that raise questions if the Jedi might have been in cohorts with them, setting the stage for his plan in the next movie. Meanwhile, we see Obi-Wan and Anakin’s friendship in full bloom now. Make their first scene an exciting action sequence on a Jedi mission where they save each others’ asses, not just some vague talk in an elevator about “a nest of gundarks.” Give them a real rapport and invest the audience in their friendship.
There can also be a “love story” here to show how Luke and Leia’s parents met, but make it just a minor subplot; maybe Anakin has to try to win a hard-to-get Padme (or whoever) over throughout the movie but doesn’t succeed until the end after he saves her or something, and their romance from then on out is implied. Again, establish a real rapport between the characters and make us care about their relationship. Don’t just tell us they are “in love” because. And skip all that shit about the Jedi not being allowed to love, there was no hint of this in the originals and it is stupid. Lucas seems to be under the impression that “forbidden” love is more romantic and meaningful, but this is not the case. Also give us actual hints that Anakin will turn to the Dark Side here. Show Palpatine beginning to manipulate him this early, show him beginning to research about the history of the Sith (put the “Darth Plagueis” thing here) and question whether the Jedi really are the “good guys,” etc. Make him doubtful and uneasy about the Jedi order.
Episode III skips ahead a few more years. Now the Clone Wars are at their height and the costs to the Republic are enormous. Terrorist attacks continue to be carried out regularly, and because the Clone Army is in short supply, men from around the galaxy must be drafted to supplement them. (Origin of Stormtroopers revealed here.) Basically, give the people a reason to be so concerned about the prospect of the war continuing that they would be willing to let Palpatine become a dictator to put a stop to it. Some clones and robots fighting each other doesn’t do that. We have to see actual consequences of the war on the people of the galaxy.
Otherwise, make the movie about Anakin’s fall as ROTS was, but make it more believable and pack more punch. Have Palpatine set up a complex machiavellian plan to make Anakin paranoid and convinced that the Jedi are out to betray him. Make Anakin feel highly protective about his family (have him already married at this point, and make Luke and Leia very young children - explains how Leia might remember her mother) and make him truly believe that the Jedi are planning to kill them. Perhaps have Palpatine point out that in the ancient past, the Jedi would “euthanize” children who showed signs that they might become too powerful and unstable, and suggest that Luke might be one such child himself and the Jedi–who are closely monitoring the children’s development–would be willing to do so again.
In fact, have Palpatine attempt to have a “Jedi” who is actually his apprentice infiltrating the organization attempt to kill Luke himself, and then have Anakin duel with and eventually kill this “Jedi,” unknowingly setting himself up to become the next Sith apprentice. Palpatine then reveals to Anakin that he is a Sith, and didn’t tell him earlier because he wanted him to discover for himself that the Sith were really “the good guys” and he had been “brainwashed” by the Jedi. Have him then tell Anakin that the Jedi were behind the terrorist attacks and the war, showing him the “proof” he planted in the last movie. Have him use all this to convince Anakin to join him and help him hunt down the Jedi - starting with Obi-Wan, to prove his loyalty. Anakin then runs to confront his friend and master, feeling extremely conflicted until, like in ROTS, he becomes convinced that Obi-Wan is attempting to turn Padme against him or even to “help” the Jedi kill his family.
Have Padme actually die as a casualty in the ensuing struggle between Anakin and Obi-Wan, driving Anakin to full-blown rage and pushing him all the way over the edge to the dark side. But in his passion, he makes mistakes and… he falls into lava or whatever. Have the movie end with Palpatine having his armies hunt down the Jedi (no “Order 66” crap though, and make the Jedi formidable opponents who don’t go down easily, and more than just Obi-Wan and Yoda go into hiding - set the stage for some EU stuff in between trilogies), taking power as the Emperor, and Obi-Wan and Yoda putting Luke/Leia into hiding. But Anakin, when he is revived as Vader, is told by Palpatine that they were killed by the Jedi, firmly burying any last hint of conflict within him and sending him into deep regret, giving him true motivation to help hunt down the remaining Jedi. This also explains how Vader did not know Leia was alive in the last movie and why he asks Palpatine how it is possible Luke was alive. Palpatine also kind of screws himself here, as his lie comes back to bite him in the OT when Vader begins to question whether he had been used once he discovers the truth. This may even explain why he wanted to overthrow Palpatine with Luke - it had really always been about his family to begin with.
The parallel between Anakin turning to the Dark Side and killing (who he believed) was a Jedi to save Luke and then turning back to the light and killing Palpatine in ROTJ for the exact same reason is also made stronger and more explicit this way. It also makes Vader a somewhat more sympathetic character who doesn’t look quite as stupid in how he was brainwashed and manipulated by Palpatine. It makes his actions and motivations a lot more understandable.
