The real story of the Clone Wars is what Timothy Zahn laid out as the backstory for the Thrawn trilogy: that the Old Republic fleet fought against an army of insane clones who were trying to take over the galaxy about 35 years before the events of the first movie. Mysterious, unnamed 'clonemasters' were responsible for growing the endless hordes of insane duplicates, and Palpatine was also involved to some extent, using it to his advantage to consolidate his political power.
However, the Clone Wars ended 15 years before he declared himself Emperor, so they were not directly tied to the fall of the Old Republic: the chaos they left in their wake set the stage for him to take over in the following years.
It probably won't happen, but I would dearly love for this story to be told in written form someday. The way I see it, this is what happened prior to the original films in their unaltered form; while the Lucas version of events is what happened prior to the SE's. These are two distinctly different universes and have nothing to do with each other in any way. In this original universe, neither Boba Fett nor the stormtroopers are clones of anyone else.