It goes without saying whatever AdY decides regarding Jar-Jar and structural PT changes will be up to him...and likely be awesome.
My take on it though, for whatever that's worth, is I'd leave Jar-Jar in and just make him a stronger, more endearing character, if that's possible. How can this be done? Cutting the abundance of his silly antics and toning him down a bit (the obvious and most common things fans mention). Other than that, jeez I don't know. Maybe by then AdY will have the help of a CG animator that can work some magic and get a bit more creative with the character.
One thing is for sure - if he's a less goofy character than that makes the power he is handed in AOTC a bit more believable.
I no longer hate the Jar-Jar character as much as I used to....which is shocking. He's just this ugly birthmark on the saga I've learned to live with I suppose.