Jonathan still works at WotC. He is a manager of the Miniatures Game.
Some context: Jonathan's idea was actually proposed for 3.0, before it came out. He mentioned it while we were developing the "look" of 3rd edition, when different people had different ideas of what that "look" should be. His idea was that the rules were actually general enough so that with only small, entirely nonsubstantive tweaks to the text (or perhaps even no tweaks to the text), we could give the rules as a whole a very different feel.
This idea, for example, would have intercepted and prevented all the long threads I've seen here about the "spiky armor 3E look" that some people really hate, because there would have been a classic fantasy version of the rules they could pick up, where the fighters look like arthurian knights and the halflings look like hobbits with hairy feet.
His point was, and I agree, that a lot of the feel of the game is defined by the presentation, not the text. Once you've done the work of putting the rules together, giving it a different presentation is a simple matter. It would be like different flavors of candy or different colored school notebooks. Everyone would have their favorite, but in the end the actual content would be the same, and it was the content we were trying to sell, not the "feel." Our agenda (speaking only for the designers) was to create a new rules system, not to give D&D a specific look or feel.
(In other words, individual groups should give the game their own feel, and no one should feel put off from adopting the content because they didn't like the art style that had been chosen.)