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The Empire

Returns and Strikes back!

An idea I had for consistently re-booting the "prequel" Star Wars trilogy-is to completely forget what was filmed! 
Although it starts of similar to the phantom menace the main thrust of the plot is that the Jedi believe the Sith have returned and are concerned about the sect targeting Anakin Skywalker. 
Anakin is a baby at this point.

But everything else....the Jedi try to battle the Sith grand master but he is such a formidable foe that they are forced to create a clone army just to fight him. They end up provoking a rebellion in the outer rim territories and a sizable anti-jedi movement in the senate. The rebels then create their own clone army and are actually invited to conquer the Jedi Centre by the senate. The sith grand master is actually Palpatines former teacher. Palpatine was rejected by the Sith when he became a senator for various blah reasons.

The senate are an advisory body and two thirds of its members are backed by various factions including the Jedi themselves and their agents. The Jedi order actually govern the core million or so systems at the center of the galaxy known as "the Republic".

Granted, I like the above idea, but it doesn't explain why Anakin would turn. 
The existing films do provide a motive but perhaps they don't really go into this in much detail. 
One would imagine that Anakin would feel that the only way to achieve victory in the clone wars is to turn to the dark side.

Let's imagine that Dooku sets up the clone army but is expelled by the Jedi for doing so. It is possible he turns to the dark side, but he isn't the leader of any rebellion. 
The leader has been Palpatine/Sidious all along, giving orders directly to the Separatists. Anakin either knows or suspects Palpatine so seeks out Dooku (hires Jango Fett for this purpose?) so he can be trained by him. 
Anakin doesn't entirely trust the Jedi order either-who had to arrange a marriage between the Queen of Naboo and Anakin just so the clone army could be paid for-so he doesn't inform them of his concerns. 
It is possible he actually spends much of the war assassinating Jedi and senators alike on Palpatine's orders. His loyalty to Palpatine and the Republic is total-while Dooku sees it as corrupt and totally beyond redemption-and, initially, believes that some senators and Jedi are traitors. This lead him, eventually, to suspect Palpatine himself of being Sith lord and being behind the war. 

A Whole New Saga

I don't know if the first trilogy can be remade but I think a starting point for the clone wars could be a brief conflict between the Jedi order and the Galactic senate. 
This conflict is resolved by senator Palpatine but then turns into a wider and more deadly war when millions of systems are left out of the Republic as a result of a few thousand deliberately seceding and the Republic actually shrinking its vast borders. The senate then asks Palpatine to take over the running of the republic and the Jedi uncover a previously hidden clone army...

Maybe...
...or

It is Qui-Gonn Jinn who establishes the clone army. 
This is purely based on a vision he has of the Sith returning and a future Galactic Civil War (the Rebellion in the second trilogy). At some point the Jedi Council find out about this, but not until after Qui-Gonn is murdered by Jedi Master Dooku. This is based on his own suspicions that the Sith have returned and that Qui-Gonn, his former comrade, is now one of that "lost order". Of course this leads to Dooku leaving the Jedi Order, declaring himself "Count" and becoming a Sith himself.
Dooku (or Maul) is captured during the clone wars and almost executed by Anakin. Palpatine convinces Anakin to spare him. Instead Dooku is put into stasis and only recovered fifty years later after Palpatine's death by Admiral 

THRAWN 

This is the basis of a remade third trilogy. 
Rey is introduced as an antagonist to Han's son Ben; who is being trained by Dooku (or Maul) under Thrawn's sponsorship. 
Eventually Jedi Leia slays Dooku aboard Thrawn's flagship while Luke (apparently) fights Ben on a planet's surface, similar to The Last Jedi-but in this situation Thrawn tries to obliterate both Luke and Ben from orbit, not realising Luke is an image. His plan is to simultaneously slay Leia and Dooku by evacuating most of the air from his flagship. This fails when Rey arrives to rescue Leia after she has slain Dooku.

Some background: the Rebellion apparently wins but the New Republic faces difficulties from its inception, particularly when Coruscant disappears (it's cloaked) and then Luke Skywalker (he's captured trying to recruit the Nightsisters). 
Leia Solo is forced to choose between leading what is left of this new galactic government or trying to finish where Luke started in finding and training a new generation of Jedi
(AndOr)
Chancellor Leia Organa-Solo is in the position Palpatine is in during the first trilogy. No-one knows she is the Last Jedi until (she is) exposed in the third film; at which she does the honorable thing and resigns as leader of the Restored Republic.

late edit:

In the Republic the senate has total sovereignty. The Republic is a dictatorship, or would be if the senate agreed on anything.
The Republic has no constitution so the senate can legalise or prohibit ANYTHING.
But is their any point boring people with this?

I think there is one plot point which explains why the Jedi try to overthrown Palpatine and why Anakin turns to the dark side: the senate arranged the clone war in order to both conquer/subdue the Outer Rim and to find out which type of soldiers work best: clones or droid troops. PS the Jedi find out when Anakin does that Palpatine controls the Trade Federation as Sidious, which controls most of the senate. This doesn’t need a lot of exposition to explain while leaving all the battles intact.

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