As bad as this may sound, Padme has to die. First Anakin loses his mother in his arms and that drives him to the dark side a little bit and when Padme dies in his arms too, that would be the two people he cared the most about dying in his arms, because he was not powerful enough to save them. That would drive anybody to the darkside, plus I think it'll be set up by Palpatine or Dooku so it looks like the Jedi, OB1 in particular, are the ones responsible.
Does anyone have a theory on how the Rebel Alliance starts? In Ep. II Bail Organa is best friends with Palpatine, right? I think that toward the end of Ep. III Bail will find out that Palpy is evil and will rebel against him and start an alliance consisting of the jedis and other people. Most of the Jedi will be wiped out, causing the Rebel Alliance to go into hiding for awhile.
Actually, in AOTC I believe Palpy and Organa are more political allies than friends....
Spoiler:I think that in EpIII when Palpatine grabs more and more power Bail and Mon Mothma will realize his evilness and decide to form the Rebel Alliance....in EpII everyone still trusts and respects Palpatine
actually Bail looked a bit sick of the idea of a clone army at the end of AOTC