It doesn't take much to make lil Ani more interesting, just cut all the apologies.
Are you proposing Qui gon sacrifices himself in order to guide ani to save the day? that would be a fresh tie to the OT that actually makes sense rather than a backhand remark in the closing moments of the film. - Ala Yoda's muddied eplanation of force ghosts to obi wan.
I love yr idea of slimming down the climax of the movie and giving more focus to each, And wow - the idea of moving the gungan / droid battle to earlier in the film actually makes it seem interesting.
Re: Jar Jar - remember yr telling the story, so he doesn't have to be an exile at all if that means you have to work around it.
Re: yr Amida/ Padme issue. You could seriously consider not mentioning it. Back in the OT hardly anything was explained [within the films]. I know this is a hardly simple but what of keeping the padme / boss nass scene but reducing him to the sole gungan present? it would help since he's got his mug alover the big plan scenes later on. just throwing that out there.
I liked that Ani fought with greedo. I didn't like that the film was like "hey everybody, this is Greedo, okay?!".
And i think i prefer Maul being a bit of a suprise them rather than have been sitting around just waiting for thm to finally show up.