OK this one kept me up last night )I frickin hate it when that happens!)
the one thing the PT lakes is symmetry, GL has always said he wanted the movies to act like stanza's in a poem where they echo each other, well for me the PT doesn't really do that it doesn't seem to have a beginning middle and end.
here is what I would do
TPM -
One radical idea I saw mentioned on here was having Sidious removed from the movie entirely. and give Maul a more centralized role.
All the obvious stuff, like 3PO NOT being built by Anakin but have him as a aid to the Queen (none speaking part) on the ship, JARJAR re dubbed to not sound like a total turd and the battle droids dialog removed almost entirely. Make it a much bigger battle in space at the end and have anakin intend to do all the things he does no more OOPs crap
As I stated some days before on here - have Palpatine and Yoda have a meeting at the end of the movie where they discuss the impending threat that the separatists may cause and that a clone army may be the only answer (ADR may very well be required for that one I know), Dooku could be in this meeting as well for when Obi wan calls to inform them of the sith's death. (I would love to hear what you guys think of this BTW)
AotC -
Have the Deleted scene of Padmé looking out the window at Anakin (this is the only scene filmed that I think shows Padmé to have any hint of an attraction to him and needs to go back in.
When Anakin is in the garage confessing the murder of the sand people have him confess to Palpatine and then have Padmé come in as he collapse to the ground saying "I miss her so much"- so she falls for someone who is heartbroken and not a mass murdering psychopath! (this will add some of the above mentioned symmetry to it and RotS)
Again have 3PO in the background of the apartment scenes in a couple of shots
As for RotS -
I am going to watch BOBGarcia's edit before I can really comment on this on
again please let me know what you guys think of this
Have Anakin