How I would have made the prequels
1. Padme would not be a Queen from Naboo, she would be a force-sensitive Padawan who is training alongside Anakin.
2. Yoda is Obi-Wan's master, not Qui-Gon. (They told us in ESB that Yoda was the one who trained Obi-Wan).
3. Darth Maul is Palpatine's apprentice throughout all three movies. No Dooku or Grievous, they are unnecessary changes made to sell action figures.
4. Padme and Anakin fall in love, which is against Jedi rules.
5. After being told that he can't love his fellow Jedi Padme, Anakin becomes angry and begins making his way toward the dark side.
6. There is no rule of two. There are just as many Sith as Jedi.
7. The Battle of Geonosis is between an army of Jedi and an army of Sith, rather than droids.
8. Jar Jar either doesn't exist, or has a completely different personality and speech pattern, one more like a pirate/bouncer.
9. Anakin becomes Darth Vader after killing Darth Maul.
10. We see Darth Vader receive his new red lightsaber at the end of Episode 3.
11. We see a glimpse of Han as a boy, being raised by Wookies.
12. We get a glimpse into the future in Episode 3, seeing a child/tween Luke and Leia on Tatooine and Alderaan respectively.