So I think it goes without saying that the prequels fell short of what people were anticipating.

What was your favorite concept for how the prequels should have unfolded?

What were the Clone Wars actually?
How did the Republic fall and the Empire form?
What was Palpatine’s actual backstory? (He was a puppet in ANH, ultimately becoming a Sith Lord in ROTJ)
What were the Jedi really like?

For myself, I think that the cobbled together nature of the original trilogy works for 4-6 but creates plot complications. They are easy to overlook when they’re just backstory but become hard to reconcile when actually dramatizing them. There’s two kinds of problems, the canon established in the OT and the unforced errors Lucas introduced. A canon problem is how it doesn’t make any sense to hide Anakin Skywalker’s son with his uncle under his given name. An unforced error is introducing Anakin as a child when it was clearly stated that when they met he was already the greatest pilot in the galaxy. Another unforced error is deciding that Kenobi’s desert attire, similar to what others were wearing on Tatooie, now represents Jedi robes. This would be akin to the Nazis winning WWII and the last rabbi is in hiding but still dressed like an ultra-orthodox on his way to temple.

I think the basic structure of the prequels should have been like this:
Episode 1 – thematically like ANH. Introduced to a 20-something Anakin who is a spitting image of young Luke. A triumphant adventure, bonding with Obi-Wan, feels like there’s great things in store for these two. Would be set during the last Clone War.

Episode 2 – The tragedy of Anakin Skywalker. The wars have ended and the Republic is busy losing the peace. He’s married the love of his life in the period between the first and second films. He’s becoming disenchanted with the obvious flaws of the Republic and he’s not wrong, those are serious flaws. He meets Palpatine, a sector governor during the last war who has now entered the Senate. The movie follows his disaffection from the Jedi, from Obi-Wan and his conversion to Palpatine’s point of view. Palpatine is not cackling crazy evil here, he’s presenting a very cynical and Machiavellian take on democracy and self-rule and the Republic’s rulers do little to provide a good counter argument. Palpatine becomes the leader of a populist reform movement with obvious fascist echoes and the Jedi eventually are moved to enter domestic politics and oppose it. The movie ends with the famous duel and Anakin is left for dead and he clearly must be, look at those injuries.

Episode 3 – Jedi Holocaust. You have the Jedi resistance treated as a Reichstag Fire moment and Palpatine is given emergency powers. It’s pretty much like a horror movie as the Jedi try to escape the borders of the Republic as they are hunted down. Pretty much every Jedi we meet in this film dies. Vader is introduced but is treated as a mystery. Who is this guy? He comes out of nowhere, he’s radiating the Dark Side like a reactor in meltdown and he’s slaughtering anyone who stands in his way. This mystery is hinted at when Obi-Wan survives an encounter and appears shaken, like he recognized him but it’s not confirmed because the mystery should be preserved for anyone watching the whole series in chronological order for the first time. The film would end with Palpatine being declared Emperor and the Republic becoming an Empire.