XLR inputs are the exact kinds of advanced video features a 6D would have â€” physical ones that are so substantial to a camera (XLR inputs are pretty large) that it would only be wise to include if they were going market toward video people.
As far as firmware goes, the entire line is probably going to be consistent. But what could some of these other physical things be? A rugged articulating screen, a video optimized sensor that focuses on moire instead of ISO, a hybrid mount that could fit EF and PL lenses, more video-friendly ergonomics. Though are just shots in the dark, but that's how Canon could fill the space between the 5D and the 7D with a video-oriented camera.