One of the biggest flaws of the whole saga is in my opinion the way the clone army is discovered coincidentally by the jedi and them not questioning its creation.
They are facing the threat of war and don’t question the secret creation of an army and how could Palpatines plan to subjugate the galaxy include coincidences.

Well the idea that I had to resolve this mistakes is to change the plot of episode II (and maybe episode I) so that it resembles the July Crisis, which started World War I.

There are already some similarities between episode II and the July Crisis, like an assassination attempt on a prince/senator (former queen) or a political tension of alliances falling apart/the Separatist leaving the Republic as a circumstances leading to the crisis and eventually World War I/the Clone Wars.

The creation of the clone army could be moved to episode I, as a reaction to the crisis on Naboo and to mimic the arming the German Empire did in the early 20th Century. It would also imply that nobody was expecting the Clone Wars, but something like another Battle of Naboo (like nobody was expecting World War I, but another Balkan War).