I do like the Ebon Hawk, particularly because it was a private vessel. With the Normandy (at least, the SR-1), you always got the feeling it was a military vessel that was Alliance property, and you were just borrowing it.
Points for the Mako, though. The Mako had a personality I bonded with.
The SR-2 felt more like a base to return to than a vessel, but at the same time, it felt like enemy territory. The SR-2(A) was finally free of that feeling with the return of the blue, but having the war room felt like it was more committed to the war effort than it was you. You were just along for the ride. Again.
Now that I think about it, I suppose that even though the SR-1 was a tactical downgrade, it was my favorite Normandy. I actually was yelling at whoever blasted it apart in the opening of ME2. By the time ME3 rolled around, I didn't care if the Normandy SR-2(A) fell apart just so long as it got the job done for me. I guess the old Normandy gets more points for that, if anything.
But the Hawk? The Hawk felt like home.
You could stick stuff in the cargo hold. It had a work bench (and a lab table in II). It had a gun you could shoot. It may not have had all the fancy galactic displays or the sleek light panels, but it got the job done and could land on the surface of planets for your convenience.