I have a way to make the Gungans do what they're supposed to at that point in the story when we meet them.
There should be a growing sense for Qui Gonn that something strange is afoot, something at a cosmic "Force" type level. That's what this movie's about -- a simple assignment for Qui Gonn turns out to have galactic importance -- on the political level and on the Jedi level.
So meeting Gungans who are just dumb symbiots with the Naboo-- and Boss Nass, a leader who is by definition "weak minded" because the force trick works on him -- it truly undermines the sense of importance this story needs.
Solution -- make the Gungans wise. Not Jar Jar, per se, but the Gungans.
Imagine: Jar Jar takes the Jedi to the underwater city. They are taken to Boss Nass.
His first line (more or less)? "The council sent two jedi? Just two?" See, he's ahead of the game.
He continues: "To handle this? Their eyes have gone blind to the living Force. Two Jedi when an army couldn't win. This is the end, the falling of the dark times. You must sense it too."
He looks at Qui Gonn. "Yes, I can tell that you do."
Confused, Qui Gonn tries to bring things to order: "A droid army is about to attack the Naboo. We must warn them."
Boss Nass continues along this new, Force embracing, wisened way. He represents the true, natural order as opposed to the beuraucratic Jedi Council. His flaw is that he's a little too resigned to fate as we meet him:
Boss Nass (more or less): "The droid ships have been here a long time. Their purpose is not what it seems, but it was already too late before they arrived. And the Naboo? They have spent all our good will. When they took our Kaiber Crystal, it was the final straw. You may go to them, if you wish Jedi. If Jar Jar owes you a life-debt, he may go with you. But you will not win. The end is near. The Gungan will face it with honor. Not with our head in the sand like the Naboo -- or the Jedi Council."
This reinforces the disturbance that Obi Wan and Qui Gonn repeatedly mention -- the rise of the Sith. When the Naboo finally reach out to Nass, he is already preparing his army to attack-- but he likes the Queen's gumption and agrees to team up with her. In the end, she gives him back the crystal and things seem to be on an upswing. He does not mention his doubts again -- in fact, he's done what it takes to save his planet from the Sith (as I don't believe the Sith ever mention attacking Naboo again, right?).
This makes the trip to Gungan city a foreshadowing device and a good set up for the Gungan massacre we plan in the third act.
Just thought I should post a little about what I'm thinking. More later...