I think he'll have a bigger part in E3 than he did in Clones.
He'll come full circle and serve his purpose.
In the escape of Padme, the kids will be separated per Yoda's orders.
Ki-Adi Mundi (most likely) or another Jedi will take the baby Luke (I stress Luke, not Leia) and the Naboo will offer defense of their former / current Senator.
Before that I think that Padme will really loathe JarJar. She will say that she would have rather died on Geonosis, sacraficing herself (like a true hero character would) than have the Military Creation Act she opposed, singularly implemented by JarJar's reversal of Naboo's position, just to save her life!
Palpatine wanted her dead or out of the picture just for that reason anyway.
So JarJar will be really annoying trying to make it up to her, and she'll blow him off, until in this crisis, JarJar will redeem himself.
He'll get baby Luke with some Naboo and Ki-Adi Mundi. But perhaps by scanning lifeforms for midichlorians or whatever, they will be able to track them, so JarJar takes Luke with instructions to get him to Obi-Wan Kenobi (who JarJar obviously likes and trusts) while Ki-Adi Mundi dies sacraficing himself as a decoy.
Then it's JarJar's final nobel act - to sacrafice HIMSELF as a decoy, just like Padme would have done - while Obi-Wan gets away with Luke.
Now I think the audience will still cheer when JarJar dies, but Classic SW would not be possible without him:
He initiated Palpatine's martial law and authorized the Military Creation Act in doing so - empowering the bad guys.
and He saved Luke Skywalker, eventually becoming the catalyst to Anakin's fulfilling the prophesy to save his son - thus empowering the good guys.
One could say that JarJar brought balance to the Force.
Or one could say that when his ship is atomized, he brought back a sense of relief to the entire galaxy and the viewing audience!