Re: What would you have done differently?
Just a few:
1. Older Anakin
2. Episode I closer to the Clone Wars timeline, if not already at the beginning/during the CW. With Episode II could have basically been anything from the animated series...with Ep III mainly the same.
3.Darth Maul as a series (PT) long antagonist...doing a new villain each film left left little time to develop those new characters...having one main antagonist (besides Sidious of course), they could have at least maybe given some more backstory to Darth Maul or whomever---or at least the opportunity to learn and expand upon why the baddies are bad---no chilling music cues, or characters dreading and informing us he's bad...
4. No over reliance on the EU---I think the PT suffered from having to use the EU to fill in gaps. Something mentioned in the films (namedropping characters, planets, battles, etc)---you could probably read about it...or play it...etc...I ain't got time for that...
I'll try to think of a few more, I'm a little ill, and just trying to pass the time right now.