The prequels should have started during the clone wars - which should've been going on for a number of years, with a much older Annakin - there were rumours of Gabriel Byrne taking the role. I thought Obi-wan and Annakin should've been in their 40's, as Alec Guiness looks about 70 in Star Wars.
They should've been epic war films, with the same Kurosawa influence running through them. Annakin should've been turned to the darkside because of the power he felt, not through a love story. The films should've had R2-D2 and C-3PO in them much like the ST, as servants who sometimes save the day and comment on things.
Complex political arguments could have still played a part, and the formation of the empire could've been shown in a much more dynamic way.
Jedi's should've been much cooler! Not a bunch of idiots running around twirling lightsabers - they're supposed to be Samurai after all. Definitely needed a Han Solo type character - could've been a woman, missed opportunity. The cynical character could've even been Annakin himself.
We all know that Annakin turns into Darth Vader, but it would have been great if it was somehow an unexpected turn of events that led to this - he takes a path that the audience would also choose. We know the ending, but getting there could have been really something amazing. Very tough to come up with that type of situation, but there you go.
Obviously they should've been looser, a few adlibs, more life in them. They should've been made for adults.