TV's Frink said:

I don't know, her performance as the Queen is so stilted and different from her Padme performance, I don't think it's too much of a stretch to have Portman in two roles as completely different people.

Is there a way to keep the idea that keira is a decoy but that the Portman queen is not Padme?

I don't think its a good idea to make them into two different characters. If you did that, then the story for Attack of the Clones would not make sense.

I want the edit to be easily integrated into the rest of the prequels.

Jar Jar, for example, can be removed entirely and not affect the storyline.