So RedLetterMedia's new review has some interesting points about how the prequels could be improved.
Skip to around the 30 min point of part 1 and you'll see what I mean. Some would be relatively simple to pull off e.g. the general mood of coruscant with decaying buildings, less air traffic and more poverty along with Palpatine's propoganda over megaphones.
It's completely true (though it's never occurred to me before his review) that the effects of the war just aren't felt on Coruscant at all. Life just carries on as normal, which is ridiculous!
Then there's the suggestion that the clones should have been the opposing side (or at least utilized for the purpose of espionage and/or infiltration by cloning and replacing high ranking Republic officials - just like in Harry potter where you had people at the Ministry of Magic being put under the imperius curse) and all the republic troopers would just be regular soldiers forced into service, which I've always thought is how it should've been.
This of course would probably be impossible.