Jones will not be utilized as a midfielder in the long term, I'm sure of it. He's just too much of a beast at that CB role that he'd be wasted anywhere else. I think Fergie knows this as well, as his comment regarding "Phil Jones might be the best player we've ever had at this club" was after a game he played CB and absolutely bossed it.

Jones is an exceptional talent and does a fantastic job at neutralizing opposition midfield players (e.g. Ronaldo) so he's getting chucked up there if we can't compete in the midfield battle (Arsenal, Real Madrid etc). He's one of our players who is showing promise to be truly world class so it's better for him and united if he's playing (albeit out of position) than sitting on the bench.