Saw the movie for the 2nd time last night - Carol Marcus definitely says "He's developed some sort of transwarp drive".
Also, the lock Kirk uses to open the door to the warp core reminded me a lot of the maglock used by Picard to release the deflector dish in First Contact.
Regarding the USS Vengeance model...I pick up on this last night...when Kirk asks Khan "Tell me everything you know about that ship" Khan responds "Dreadnaught class ...Twice the size three times the speed" I took that to mean initially that he was comparing it to the Enterprise..However, I think he was saying Dreadnaught class but twice the size, three times the speed of a regular Dreadnaught class ship. If this was so, it wouldn't be odd to have a model of a regular Dreadnaught class on his desk.
Just my thought.
My first time back here since September 2010...missed you all!!
EDIT: Not that it has much bearing on the screen version, but in the novelization, they reference Praxis. Therefore, I'm guessing the destroyed moon around Kronos, is supposed to be the Praxis of Undiscovered Country fame.