The Gungans should have their own language. This would be a great way of throwing in new dialogue and somewhat alter their personality. Jar Jar, crazy as it sounds should be played by a woman (albeit in a deepened voice).

Something else we need is people calling Obi-Wan "Ben". Most likely General Grievous and many of the non-Jedi characters.

Likewise the multiple battles in The Phantom Menace ought to be reduced by:

Removing everything in the Gungan battle after the droids enter the shield. We would only know their fate in the ending.
Anakin not going into space and blowing the Federation ship. I feel this achievement was given way too much importance whereas the real focus should be the Duel.
Having the Queen and her troupes sneaking into the palace rather than blowing and things and making enough noise for the Viceroy to notice.