darkSpyro

2) The name could perhaps provide some clue. Lucas is often not particularly subtle with his naming choices while still not making them seem unnatural. Skywalker, Solo, Darth Vader, etc. So can the very name Jar Jar Binks help solidify this theory?

Let's take them in order. Jar can mean a number of things. From Merriam-Webster.com, "to have a harsh or unpleasant effect on someone or something", "to hit or shake something forcefully", "to make someone feel uneasy". A couple of secondary meanings given are "an unsettling shock", "an unpleasant break or conflict in rhythm, flow, or transition".
Now for Binks. My best guess is that Lucas was drawing on another already existing source as his inspiration for Binks. The popular fantasy world of Xanth, created by Piers Anthony and with its first book published in 1977. The main character of the first two books and a recurring character through other books in the series is...Bink. Copy/Pasted from Wikipedia, here is Bink's description.

"Bink is the Magician of Magical Invulnerability and the main character in the first two novels of the Xanth series, A Spell for Chameleon and The Source of Magic. He is the son of Roland of the High Council and Bianca. He serves as king pro-tem during Trent's reign.

Bink is banished for not possessing a magic talent when, in fact, he does possess magical ability. Bink's magic does not want to be known because, if it were, those of non-magical means would injure Bink and his family, with the magic being indirectly responsible. Hence, in order to keep itself hidden, Bink's magic works in quiet ways, by seeming coincidence, and very few people know of it. For example, it causes an invisible giant to walk by just as Bink was to reveal his magic whilst under a truth spell. Furthermore, Bink's magic protects him, making him seem an unusually lucky man."

So, Jar Jar Binks. With the above information, his name seems like it could actually help inform what George wanted from the character. And based on this information, if Bink is in fact the source for Jar Jar Binks' last name, then it implies a hidden magic user who appears to be just ridiculously lucky but is in fact just keeping his true nature on the down low. And the two Jars are perhaps to tell us that he will cause a dual jarring: one in the Star Wars universe when he destroys the Jedi Order and dismantles the Republic, the other in the movie audience when his true nature is finally revealed.

When he says, "Meesa called Jar Jar Binks" he's not saying, "My name is Jar Jar Binks" just saying that that's what people call him.

So the title of Phantom Menace refers to Jar Jar then? He was the real menace all along?
I can get behind this.

Yeah, Palpatine was never a "Phantom" from the audience's perspective. We all knew who the eventual Emperor was- they didn't even really bother to mask his hologram face.
Jar Jar was the intended villain that was to be "unmasked" and shock everyone, the requisite middle chapter "I am your father" calibre reveal moment.
Sadly, it didn't come to fruition. Not until this December, anyway.