A rather radical idea I was playing with: how about making Bail Organa the one who gives Palpatine his emergency powers? It eliminates the need for Jar Jar in the movie, but might also make Organa a bit more interesting character. It would give that little bump on the balcony at the end of AOTC more weight, and would also give him a motivation for starting the Rebellion.

There are some audio material The Force Unleashed cut scenes, voice by Jimmy Smits, that could be useful for this change.