If I was a new reader, and I read your version, I'd just end up being more confused. And if we were doing "reveal the details as they occur chronologically," then the Torch returning and throwing the Vision's origin in question would be written after the bit about the government dismantling him, and not before.
Was the idea of the Vision's body originally being the Torch's a retcon? The only thing I would really consider to be a retcon was Byrne trying to undo everything in the 1990s with West Coast. Should we write something like "Byrne tried retconning the Vision being the original Human Torch by bring the Human Torch back" (and Byrne has stated on his forum how he never liked the idea of the two being the same; should that be stated as well?), and then how Busiek tried to 'unretcon' it in Avengers Forever?