Okay this is just wild speculation... but Cap may not be dead. Tony had made a clone of Thor, whos to say he didn't have a clone of Cap as well? In one panel of Civil War #4 on the second to last page Tony, Reed, Wasp and Yellowjacket walk past a tube with a man with short blonde hair in it. Steve Rogers? Could Iron Man replaced Cap with a clone and the clone was the one who got shot?
The tube was never explained and it's not like Tony hasn't already done stuff like this in Civil War.
Just a theory.
It wasn't a clone. That Cap is dead. Tony and Reed are going to go into the Ultimate Universe and kidnap their Cap. Then that Cap is going to kick their ass!