Palpatine certainly is a puppetmaster, and his hand in this war will later become clear to the audience. However I made sure he does not appear until Episode II. I felt that putting him in Episode I would introduce too many foreshadowing obligations into an otherwise straightforward tale. Imagine if the following things were different about The Phantom Menace…

Anakin is at least twice as old, maybe even early 20s.
Padme’s at first not all that cracked up about leading a planet.
Alderaan instead of Naboo.
No Qui-Gon or any other Jedi Knights beyond Obi-Wan (again, they will have their time to shine in Episodes II and III).
No Palpatine yet.
Clones instead of droids fighting the Republic.
Simple reason for invading Alderaan: use it as a site to build a second Clone Machine so that Atha Prime can swamp the Republic core systems.
Start the Clone Wars right off the bat. Waiting two movies to do this was one of the PT’s biggest mistakes.

That’s what I am going for with ATG:Ep1. The “Keep it simple, stupid” approach.