I had a Biology teacher who was intent on proving that birds should not be put in the same class as reptiles. He argued, quite perswasively, that we should abolish class Avis because all of the derived characteristics birds display can be found in reptiles. Migration, feathers, territorial songs, flight, warmblooded-ness, care for young etc.
Nevertheless becase birds seem so "unreptile-like" we decide to put them in an almost honorary class.
Perhaps a similar thing is happening here? If we were able to look at apes and humans more objectively we might not have these problems.
Is genetic analysis objective enough? Or does it miss the "important" differnces in functional abilites as bencip seems to suggest?