I don't mean this in any condescending way, but you've brought up a valid point that has been made time and time again.
There are elements of "poor design" found in pretty much every organism that are the result of body plans being limited by the body plans of their ancestors.
So far, the creationists have no real answer to those problems except for saying, "that the way God wanted to do it. There are certain obstacles that God wants us to overcome. Etc, etc, etc." For them, the traits that work really well are "evidence of design" and the traits that are redundant or sub-optimal are that way "because God didn't want to make life too easy." There's really no logical way to argue against this beyond trying to point out the fallacies of their logic, because no amount of biological evidence will suffice.
We have many intuitions in our life and the point is that many of these intuitions are wrong. The question is, are we going to test those intuitions?
-Dan Ariely