Ooo, fun thread! I would pretty much scrap all 3 movies and take it from the top, and I would DEFINITELY eliminate all the connections between Yoda and Chewbacca, C3PO and Anakin, some of the planets, etc.:

TPM:
-Starting Anakin out as a young adult and briefly touching on his childhood, but getting totally rid of the whole virgin birth stuff; retains the mystery of his character.
-Totally scrapping the whole Midichlorians (sp?) thing.
-Touch on the politics and the behind the scenes corruption of the Republic.

AOTC:
-Showing a MUCH BETTER version of Anakin's transformation, and a MUCH BETTER love story between him and Padme. Maybe throw Obi-Wan in there too to cover the jealousy aspect; could've been an interesting sub-plot.
-A MUCH BETTER clone war, complete with the Mandalorian Warriors (and FYI, the lack of this was one of the most disappointing things about AOTC to me).
-Maybe show Chewbacca/the Wookies back story; would've been easy to tie in w/ the Mandalorians.
-Padme getting pregnant and hiding it from Anakin because she can already see the change in him.

ROTS:
-Anakin becoming Darth Vader much sooner in the movie and fighting and destroying Jedis like Mace Windu.
-Shown more of the Emperor and the rise of the Empire.
-LEFT IN THE REBELLION SCENES and expanded on them!
-Luke and Leia being born, but Vader not really knowing about them. You would tell through the 2nd and 3rd movies he suspects it, but A) never really sure b) doesn't know there are twins and C) may even think the child is Obi-Wan's; goes back to my whole sub-plot thing.

Also, I would've named each movie something different probably, but I am using the original titles for the ease of reference.