Whatever you do, please, please, please, do not reintroduce the "Birth of the rebelion" and "Yoda lands on Dagobah" scenes just because they are there, since we all agree that there is no need to explain everything.

I guess, besides any changes that you might want to do, the four main "scenes" that need to be reedited are the coruscant battle, the confrontation between obiwan and grievous, the whole mace windu palpatine anakin and the whole final battle (padme and anakin, yoda and sidious and obiwan anakin)

I guess those 4 scenes are the ones that are most poorly directed, because they are long, distracting, or because George Lucas forgot what the point of the scenes were and got distracted with background robots and special effects.