Lost in what sense? Are they going to the national championship? No, definitely not. Can they still make it to a BCS bowl? Definitely. This team went 8-5 under Tommy with a much worse defense, a worse offensive line, but better running backs. Tommy has obviously improved since then, and I still don't see why a 9-3 at worse season is considered lost.
We also no longer have any of the guys Tommy threw to. He had some juju with Eifert and Floyd, Toma and even Goodman that we don't have any more.
Also just lost a couple of NFL-caliber RBs.