I would have liked to see more of Darth Vader. Just imagine for a moment that Anakin had fallen into the lava by the end of Episode II and had spent all of Episode III with the Mask on, surrounded by Stromtroopers, and just generally being the evil doer he was by Episode IV - If he had killed the younglings with the mask on, in the suit, that would have made it so much better. That's the prequel I wanted to see. Really for me, it was only at the very end of Episode III, when Vader is on the bridge with Tarkin, that I felt any connection to the original Trilogy - that moment gave me goosebumps! So, more of that would have been great.
Also, Real sets! Real Props! Less CGI! I have yet to see a CGI Jabba that is as half as convincing as the massive foam-rubber puppet built 30 years ago. A real set, with something physical to work with not only gets a much better performance from the actors but also generates an atmosphere - something a computer just can't recreate convincingly - or at least it couldn't when the prequels were shot. Perhaps it can now.