I've always wondered too. Would be nice if the console had compartments in it. Moss Mustang sells a divider to put compartments in your glove box. Something similar would be nice for the console. The space you're talking about would be great if something actually fit in it. I've tried many things and it's too small.
Ipod holder? I have a 2005 which doesn't have the connections. Also, Mustangs for years have had the clip, so it can't be intended for that purpose though it may work.
What DID Ford have in mind?
I've wondered the same thing. So far, the only thing that I can find that will fit in the clip is my ipod mini. But even that is a little too thin, and falls out of the clip from time to time.
I'm sure at some point, somebody in the aftermarket will find a way to attach something to the clips, or make them useful somehow. I can't think of anything myself, but I wouldn't be surprised if there will be something to stick in there....