The OOT never gave me the impression that the Stormtroopers were clones. They were just soldiers in armour. My concept of the Clone Wars was that clones of people were created and used as spies and assassins and to spread lies, causing confusion and paranoia. Not thousands and thousands of troops but a smaller flood of clones which caused everyone to start distrusting the person next to them, leading to a disintegration of trust.
This idea can be used as the way the Emperor attacks the Republic from within. With distrust everywhere, the Senate blindly accept his offer of strong leadership and, once elected President (to use the position initially held by him in the prologue of ADF's novelisation of SW '77), he starts to demolish the Republic and erect the Empire one motion at a time.
The Jedi, through their sensitivity to the Force, can sense the clones and tell them apart from the person they have been cloned from. They start to defend the Republic from the clones. Palpatine counters this with a series of "outrages" perpetrated by clones of Jedi and contrives to have the Senate agree to allowing the Lords of the Sith deal with the Jedi "threat". Soon, he is openly declaring the Jedi as being the originators of the clones and that the Jedi were plotting to seize control of the Republic. The Sith begin the systematic "cleansing" of the Jedi Order from the galaxy.
Some initial ideas - any thoughts?