The controversy about the existence of the phylotypic stage is more than some bickering about whether one blobby, slimy fish-thing looks more like a Roswell alien than another one does. It's about whether the phylotypic stage means something, whether it tells us something important about development and how developmental changes contribute to evolution.

If you have only read the more superficial descriptions of intelligent design theory, and specifically the descriptions of irreducible complexity, you might (reasonably) conclude that Michael Behe and other devotees of ID have claimed that any precise interaction between two biological components (two parts of a flagellum, two enzymes in the blood clotting cascade, or a hormone and its receptor) cannot arise through standard Darwinian evolution.