Here are the changes I would have made to C-3PO's story in the PT:
1. When we first meet him, he is just an anonymous protocol droid serving in the Senate delegation from Naboo (under Palpatine). This would be a nice parallel to R2's origins, and it would allow us to see him "in action."
2. As a corollary to #1, give him something to do! In the OT, he's translating and interfacing between people. And in doing so, there is the natural chance for some comic relief. In the PT, he doesn't have anything "to do," so attempts at comic relief are forced upon him.
3. Also, if he is the translator for Naboo senators, that would allow for his friendship with R2 to mature organically, since R2 is Padme's (then Anakin's) droid.
4. No head-swapping-battle-droid crap.
I also wish there were a way around the whole "memory erase" thing, but I'm afraid there is not. I really like the idea of R2 and 3PO meeting on Coruscant for the first time (after Queen Amidala flees Naboo), and then remaining friends until the end. But, I can't think of anyway to have him actively participate in the PT and keep any measure of plausibility and character in the OT unless he gets "rebooted."
I wish that R2's "hero" scene in Attack of the Clones was better. Really, the only thing he did in the whole movie was save Padme from molten steel in the droid foundry, and that felt really tacked-on. It was like, "whoops, we forgot the R2-saves-the-day moment, better come up with one quick." Plus the fact that it was our introduction to his (controversial) rocket boosters made it all the more suspect.
I have an idea for how to make it better, but I think that post will need to wait for another day.