Sorry I kinda made it sound like you see them on the federation ship... No Jedi seen until they jump off the overpass....

My other thought was a stronger reason for the federation... Here's the kicker... We don't know why they are invading until the end when the republic has come to arrest the neimodians, and then they discover what they were after all along. Clones. You could have a shot at the end where Palpatine walks into the clone chamber where they have perfected the technology.

Then in Ep. 2 you could stae via crawl that the republic relocated the clone tech to a more fortified world that could protect it from those who would exploit, while all the while it's in the hands of the enemy.