For me the new triology just started wrong. Leaving aside such abominations as midiclorians and Anakin's virgin birth. My biggest problem is that Obi-wan and Anakin are just to far apart in age.
When Obi-wan said in ANH that Anakin was already a great pilot, when he met him; I had always assumed that he meant that he was a top fighter pilot during the clone wars. And that they met during the CW and became fast friends.
So here what I would do:
The First Film
1. TPM never happened. Force sensitives can be discovered and trained at any age. Anakin has actually parents (no virgin births). The force is completely mystical, and incompletely understood.
2. The first movie opens with the clone wars starting the for the same reasons Palpatine pulling strings etc. Start the war with CIS attacking a worthy planet (Kuat, Correlia, or Alderan).
3. No Freaking Droid armies (but droids are used for fire support, SD-10's baby!

3. I'd have the movie follow to different tacks:
Obi-wan (the freshly mented Jedi knight) story; Just released to operate on his own by his master YODA.
Anakins story as a young volunteer to the Republic's fighter corp. Detailing his training on Cardia (yes the Republic has an actual military in my version). Anakin should be cocky as hell, think Han Solo, or Roy Fokker (from Macross).
4. I wouldn't even have them meet until the end the of the first film and Anakin would be completely un-impressed by Obi-wan being a Jedi (similar to Han's attitude in ANH).
The Second Film
1. The war continues....3-4 years latter.
2. Anakin and Obi-wan have become friends.
3. A rather arrogant Obi-wan offers to train Anakin, who would resist his attempts to convert him until he is forced to call on the force to save his life.
4. Anakin meets Padame - yadda yadda (insert a believable love story here)

5. Anakin's racked up over a thousand kills, and is starting to go all dark.
The Third Film
More later.... But in my version it would be very clear that if Padame had lived Anakin would never have fallen.