Of course, Palpatine was probably in charge of defense for the republic.
Either way, the "twist" of having the clones serve as "good guys" in AotC was a poor choice, and it really raised questions about how much the Jedi value human freedom. The only redeeming things I've seen come out of Lucas' decision to make the Jedi lead the clone army were the cool special forces troopers in the Clone Wars cartoons. I mean, when I used to play Star Wars as a kid, my Stormtroopers were always unique and badass even though they were totally disposable in the films, so it was nice to see a few cartoon troopers who *almost* had individual personalities.