The way that article is written, by "we're going to do the Phantom Menace," Lucas means that they're going to do a film that has mega high expectations and probably isn't going to please all of the fans. That's my take anyway.

Furthermore, I had no idea what a "McGuffin" was, so I looked it up:

Main Entry: McGuffin
Part of Speech: noun
Definition: in film, a plot device that has no specific meaning or purpose other than to advance the story; any situation that motivates the action of a film either artificially or substantively; also written MacGuffin
Etymology: Alfred Hitchcock's term, based on a story where this device was used in a story set on a Scottish train

So it sounds like they're basically going to take a previously unimportant plot point from one of the first three films and make that the premise of Indy 4.