I haven't seen any statistics to confirm this belief, but it seemed pretty clear that Miami played a lot more 2-deep last season. Jones plays his best football in the box. Not to bring up the terrible past, but Jones is kind of like a better version of Gibril Wilson. When he's playing close to the line of scrimmage, he can make plays. The deeper he plays, the more pedestrian he looks. In the first half against New Orleans (during the season the Saints won the SB and we gave up that big lead), Miami played Wilson in the box, and he made plays.
Thomas, FWIW, has the athleticism to play at a high level - the necessary physical tools (4.51, 10'04 broad, 38" vert). That doesn't mean he's going to beat out Jones, and it's an unlikely scenario, but if Miami knew they planned on playing Jones in more 2-deep looks, they should have never given him that contract.