Lucas doesn’t care too terribly much that some folks have a problem with Jar Jar. “I think the comic-relief character is an important dramatic device,” he says. “Some of the fans that want The Phantom Menace to be The Terminator don’t like the idea that there are comic characters in it. I certainly am not going to make a grim bloodfest out of Star Wars.”
I think Lucas is wrong. While there may be some fans for whom this is true, I think most fans who don’t like Jar Jar don’t like him because this comic-relief character is much too much the focus of The Phantom Menace. He detracts/distracts from the story rather than enhancing it.
(Which is why I’d love to see The Phantom Edit.)
I also suspect this is a direct result of Lucas experimenting with ways of filmmaking—doing pre-production, production, and post-production somewhat concurrently. My guess is that this process obscured the “big picture” from the filmmakers.