Order 66 was used after about 3 years of fighting during the Clone Wars. The primary goal was to wipe out the Jedi. When it was given, the excuse was that there were signs of a Jedi rebellion against the Republic, which was an entirely manufactured reason.

If Palpatine was just going to make up a reason, what did he gain by allowing the Clone Wars to proceed for a full 3 years? While he's a Sith, and therefore evil, and isn't going to care about lives lost, he's still losing resources, such as the clone troopers that will be able to serve him as stormtroopers.

Why did he need to wait so long before giving Order 66?