That plot hole in the Prequel Trilogy makes them hard to watch.
This is not an EU topic - look at it from the perspective of someone watching these films in order for the first time.
When Obi-Wans asks Yoda who could've emptied information from the archives - Yoda says it's a dangerous and disturbing puzzle. That only a Jedi could've erased those files.
According to the Kaminoans, Jedi Master Sifo-Dyas placed the order for the clones at the request of the Senate. Mace says whoever ordered it did not have the authorization of the Jedi Council.
At the end of AOTC, you are left with: "So who erased those files?" and more importantly, "Why were the clones ordered and more importantly WHO?!"
Dangerous and disturbing as Yoda says.
Millions of clones just happen to be ready for war and coincidentally the Seperatists are also ready for war. No one seems to question the clones convenience - they just take 'em. The only issue they have is protocol.
It's very strange that these issues are not resolved or even addressed in ROTS. To me that's a plot hole. It is a legitimate MAJOR factor that was brought up in AOTC and then completely dropped. I always felt Star Wars was smart, but THAT issue makes the PT hard to watch - feels like my intelligence is being insulted.