Okay, so this is my interpretation of the Clone Wars. It's in-work, and subject to completely change, but this is what I'm working with.
The Clone Wars, like World War I and World War II, is a series of wars involving most of the same forces. War breaks out and armies and navies fight it out, and some sort of peace is established, but the victors of the previous wars didn't go so far as to completely decimate their enemies... meaning that war breaks out a decade or so later.
The Clone Wars collectively, and the last war as depicted in the MPT are so devastating that the Galaxy is mostly in shambles at its final conclusion. This motivates the political leaders and the people to restructure the Republic into an Empire. Sacrficing liberties in the name of peace.
At the start of the mPT, there is no Army/Navy of the Republic. Think of it like the European Union or the Allies of WWII. Each member state (planet) has some sort of military, and they work in concert at times of major crisis. During the war, one of the restructuring actions the Republic takes is to unify all allied forces. At that point in time, it's a ragtag assembly of uniforms, alien races, and ships. But as time goes on, a standard uniform and ship line begin to emerge. Also does the idea of humans being given all of the leadership roles.
The final Clone War is the setting for all of the mPT. It starts a year or so prior to the 1st movie and it concludes with the 3rd movie.
Cloning. This deserves its own thread, but let me tackle it briefly here. I'm thinking that the Republic has outlawed cloning (probably due to previous wars) and that only the enemy has cloning capability. These enemies are the Mandalorians. Not all of which are clones and there is more than one template from which the clones come. I'll leave it at this: the bad guys strengthen their numbers through cloning, and the technology and knowledge is (allegedly) destroyed at the end of the mPT.
Warfare: It was my strong desire to figure out how to do an evenly matched war. However, I don't think that's possible- at least I can't figure it out. So, similar to the Rebellion-Empire war, this war will be more of a guerilla war. Though the tables will be turned. It will be the omnipresent Republic defending against "terrorist" like attacks of the Mandalorians. The Mandalorians will seek to blow up the "Death Stars" of the Republic, just like the Rebellion did of the Empire. But they won't have Death Stars, exactly, but you know what I mean.
It's something of a surprise for the end of the first movie, but it will be shown that the Mandalorians are more of a threat- more successful and efficient- this time around. It will be revealed at the end that Dark Jedi are working with the Mandalorians, increasing their focus and power.
This knowledge (the involvment of the Dark Jedi) will bring some Jedi out of the woodwork. It's their horse to shoot, so to speak, and so they will organize to fight their own battle. The Jedi, previous to this, are not an official "group" but more like samurai who are out doing their own thing... The war causes them to organize- which makes it easier for their enemies to take them out.
Star Wars consists almost evenly of Space Battles and Ground Battles. I'm not quite sure how to really make that work, since it seems that Space would reign supreme. How quickly would the Battle of Hoth have been over if some TIE Bombers zipped in and bombed the Shield Generator instead of having to drop the walkers off a couple miles out and wait for them to saunter in. Or even better, have a Star Destroyed bomb it from space. I'm sure Hoth doesn't have a fancy planetary shield or anything. However, the Mandalorians will be trying to cripple the infrastructure of the Republic, and they would attack planets with significant mining facilities, harvest facilities, and industrial capabilities. If the Mandalorians have a mind to capture these facilities intact, then they wouldn't just bomb them from space.
Anyways... I'm rambling here... So I'll stop for now. More as I remember what else I wanted to say here, or if a discussion develops.
