You can change prequel history by altering Phantom Menace in ONE way... CHOOSE!
Keep in mind, your decision will ripple through the other two prequel movies, so choose wisely.
It would be best if you also extrapolated on how you expect your decision to affect episodes 2 and 3.
Do you:
1. Remove Jar-Jar?
2. Change Anakin from a whiny kid to a damaged 13 year old slave boy (thereby closely matching Padme's age)?
3. Allow Darth Maul to survive?
Choose your destiny.