OK, I'm no editor, so I don't know if this will work, but I think you need to cut Threepio from Episode 1 entirely. Have him gone 100%. Paint the mofo out if needs be. He serves NO purpose.
Episode 2 - Again, no threepio. What purpose does he serve apart from to get his head put on a battle droid's body and utter the line 'this is such a drag'. I think what you need to do is re-dub Threepio's Lars Farm lines to a defferent voice so that it is a different droid. He's all rusty and shit so he doesn't even look like threepio anyway. In the current version of AOTC, Anakin and Padme show up at the farm and Anakin recognises Threepio. He then says ' I'm here to see my mother'. All you need to do is cut the recognition part, so Anakin and Padme show up and say to this random droid 'I'm here to see my mother'. We then cut to inside the homestead and the scene plays out as is. If possible you could have this random Lars droid say 'and you are...?' to which Anakin replies 'I'm Anakin Skywalker'. In the next scene Owen says to Anakin 'I always expected you to show up' or something like that, so the droid would recognise the name skywalker (because of Shmi) and take Anakin to Poppa Lars to break the news of her kidnapping by the sand people.
In the original Anakin takes 3po with him when he leaves Tatooine, but there must be some way around this.
The whole nasty droid factory crapness can be cut, as can all Threepio's scenes in the latter part of the movie, then, the first time we see R2 and 3PO together in episode 3 (which is after Anakin, Obi-Wan and R2 rescue Palpatine, threepio is one of the people waiting to greet them and him and R2 have a few lines together) you just insert a line of threepio saying 'hello, I am seethreepio', artoo beeps in reply, threepio says 'pleasd to meet you' and they walk off together. The two droids then play supporting roles in episode 3 and really come into their own in the OT. It's almost like we hand them the torch to carry on the story from the prequels to the OT. I understand why George felt the need to have them in all 3 films but the point of this edit is to make it work as a 6 part saga, which at the moment it doesn't.
Artoo and Threepio's love/hate relationship in the OT will have developed during their time on the Tantive IV. Remember, back in '77 nobody knew who these two droids were, what they had been through, etc, and we all just accepted their relationship as it was. It is perfectly fine to show very little of them in episode 3 then have their relationship fully developed in 4, which is set 20 years later.