Yes, your Gungan idea is a tempting one darthpreston, but in the end I think it's cutting too much, and ruins the dynamic between Jar-Jar, the Jedi, and the other Gungans for later in the film. The flow of the scenes as you outlined does indeed work, but I think if we're to reinvent the Gungans, we need that material to work with.
I see your point, but I still don't see how much connection we get from those scenes in the underwater city. I think it would be important to re-establish the character of jar jar as a hopeless adventurer who needs to stay home in the first place. But if you keep all of the gungan city scenes, then your re-introducing the silly plot of jar jar being banished for "clumsyness" and seeing him imprisoned, then later to be freed by qui gon (through jedi mind trick no less) to take jar jar along. There is also a weird vibe going on with obi wan in this scene where he is annoyed to be taken on a pathetic, stupid creature and later points out anakin as a "pathetic lifeform"...............I just always considered obiwan to be a student that tries as hard as he can to be a good apprentice and a jedi. Well, a jedi really shouldn't go around complaining about "pathetic lifeforms", they respect all forms of life. But the whole gungan city is just really, shiny, smooth and cartoony for my taste. I don't see what character development we get from jar jar, quigon or the gungans from these scenes (at least nothing we could not get from their scene later in the movie). Besides, we need to get to the point of the movie, which now is a story of Qui Gon running into anakin and their relationship, the nemoidian fleet and their invasion, and whatever we can do with amidala's story. But that's just my opinion, i could be wrong.