I think root problem is that shuttle was starting and landing with people. They should use it just for cargo, second rocket with Apollo should have transport people from/to orbit.
They stuck out where they could be struck by stuff. They precluded the capsule eject system. They cost Shuttle tons of fuel. For a system used in only one part it's flight regime.
Why _why_ did Shuttle have wings? The Air Force insisted. So they could launch Shuttle into polar orbit from Vandenberg. Shuttle would need the wings to come _back_ to Vandenberg.
Then the Air Force withdrew from the program. Too late to get rid of the terrible wings, however.
Here's an M2-F3 landing video, as an example: http://www.youtube.com/watch?v=iaz6Bmitawo
They can do that because even on a symetrical capsule you can have lift vector control.
I can't find the video, but you can look it up with google. It is very easy to find.
The huge-giant wings were needed so Shuttle could fly cross-range back to Vandenberg after going over the pole.