Exactly this. Jar Jar's role wasn't reduced due to negative fan reaction but because the story demanded it. In what other role could he serve in Episode II other then the one he does (which is still quite significant BTW)? Was he to go with Anakin and Padme? Or Obi-Wan on his investigation? I don't think so. Similarly there's just no where to cram Jar Jar into Episode III. He had a few scenes written but they were cut because they weren't important to the story. It's the same with midi-chlorians. They weren't mentioned in Episode II because no one had a reason to mention them. Once they were important to the story again (ROTS) they were brought up.