my vote is for fifth element!

I read your treatments, way to go on that, nice work.
BBBBBBBBut i have to disagree with a few things. First off I don't think Lucas prequels are wrong. There just ham fisted, non-paying off, poorly edited etc. But the themes were just fine but very very poorly executed.

1] Unknown Vader

So with that in mind why should it be a mystery for who Vader is? What does this mean?
The idea that its Anakin's story arc is a great one. I truly feel the central theme of watching someone who should be a great hero fall is a strong classical mythology thread. So why hide that?
To pull off Anakin's fall plus the other Vader is going to take them committing some serious out doing evil. When it’s about what motives one person to do it.
Yes, we need to see Darth Maul commit something evil as early as possible but we don't need more then to see him making these acts with one caveat. Has to be a story reason. IE he’s sent to attack a base and kind of over does the killing etc.
That was a huge character failing in Lucas’s Phantom Menace if you think about it all he is really is a very well trained and brave [takes on two Jedi’s in a "fair" fight and almost kills both of them??] soldier. So we do need to see that from him at some point.
But as much as the original trilogy is about the choices that Luke makes to overcome himself we need to see Anakin’s wrong choices and how they would run parallel for a while.

This for me must also end only one way. Which would be the only reason to put in that he’s so mechanically inclined is that HE builds the suit!
So i have always pictured that one of the last scenes in the prequels would be this, as it’s the payoff for that ability. Plus and more importantly he makes his last choice as Anakin Skywalker to erase that part of himself and to be encased forever. That single image for me was one that had to happen. 

2] madalorians as a unknown outside threat.

The taxation of trade routes thing was terrible to start this but the vibe has always been that the clone wars was more a civil war then an us vs. them war.
This war is the end of in a sense a stable empire which is falling to various decadence's. Not of the roman orgy type but of the various groups that make up the ruling bodies such as the Jedi. Again he did it so badly but yes there should be a theme that something is wrong with the Jedi as well and some of them know it and deal with it in different ways. Obi wan by trying to change the way the Jedi deal with the crisis, but ends up being a catalyst for some of it,  Anakin by wanting to take advantage of it to fix it IE there is chaos only i can stop it i will over react thus fuel this farther.
Obi wan wants it to end but can’t get it to, Anakin want it to end after he’s in power, which he does. Every time the Republic loses some aspect of itself, should be fallowed by Anakin's rise in power. Even the prophesy is fine. But while hes powerful hes not the "one", its Luke. but at the same time hes is in in effect bringing balance to the force which for 1000 years has been all Jedi. Part of the Jedi issues is their dogmatic and literal interpretation of it.

One of the negative themes of this series should be the end of the singular hero, that this golden age of the Jedi is ending by the over whelming mechanization using tools like cloning, massive fleets of tie fighters, and huge warships. A star wars Battle of Agincourt. When the Jedi fall there should be that moments of like those french knights at that battle, why are we dying??

The original idea of boba fett as a Mandalorian was fine, but what were the Mandalorians? I always saw then as some remnant of the clone war period, like the first army of the republic which is replaced by the clone army. They would be part of the first mass killing of jedi as well.
They would be the army that is very tough but out of its element and be over whelmed when the enemy clones attack. It is they who would later morph into the red clad guards. [Boba Fett is wearing the armor of a madalorian commando.] His story could still be as a clone payment to Jango who’s is the prototype for the republic clone army.
[He wears a standard clone war period mandalorian suit. ]
On a last note, an image that was planned for Ep III only made it to video games comics but really should have been in the films, Jedi’s wearing clone trooper armor. That would have been one of the most iconic images of those first three. Most likely at the end of EP II.