For me the Ebon hawk felt like it was actually a character in the game not just a tool to get you from A-B , yeah you used it for travel but so much more happened there , you realy get the feeling like "this is my ship , one scratch on it and your in for untold ammounts of pain"
its the sort of ship that has so much history and personality that you wouldn't mind going down with it should you get in that situation.
With the Normandy you didn't get the same thing and personally I hated it when the game tryed to make you care about anonymous guy/gal 283 they didnt feel part of the crew they just happened to be there, with the people on the ebon hawk there was a real sense of camaraderie as you went about doing all types of stuff , with the Normandy you didn't get any of that exept with the main characters.