Jar Jar comes across like exactly what he is - George Lucas wanting to pat himself on the back for having the first fully CG character in a non-cartoon movie.
There are several in Phantom Menace so its not even like Jar Jar even had to be there for that reason. And I find it mildly amusing that Lucas used a really weird looking puppet instead for Yoda... then just decided to have ILM CG over the puppet like a decade later.
I don't know why they didn't just use the same puppet for Yoda from the original trilogy or, if it didn't exist anymore, make an exact replica. Yoda lives to be like 900 years old or something like that. In Phantom Menance he is like maybe 50 years younger at best which is a drop in the bucket for someone that old and yet he looks noticably different in what I assume to supposed to make him look younger. Why would he look any different? Oh yeah, George Lucas is a huge moron who couldn't even make Luke's and Leia's births consistent in Episode III with Leia's story in Return of the Jedi.
I remember when Episode I came out I was really excited for a new Star Wars and was reading up on the new movie the best I could and in interviews Lucas bragged big time about Jar Jar being an all digital character and how he was making movie history and everything like that. Obviously there are other digital characters in the movie but Jar Jar is clearly the most significant one.
Hey, maybe that is why Yoda is a puppet in that one. Being a well known character he would clearly steal the show and take attention from the other digital characters. By Episode II that would no longer matter so they could just use a CG Yoda.