Ayala's main contention came down to theology (he is Roman Catholic). He simply didn't think God would be so cruel to create creatures with imperfections. We have imperfect jaws and imperfect eyes (although the question "why would God create us with a blind spot in our vision?" was answered), and he just doesn't think God would be so shoddy, so therefore God left it up to natural causes. But it doesn't follow that just because something is imperfect, doesn't mean it isn't designed. And, if we follow the Biblical account, it is because of sin that God cursed the creation. He created everything good, but because of our sin everything is not what it was originally.
I do not see enough evidence for the Theses of Common Descent and Random Mutation and Natural Selection as the means of evolutionary development. In fact, the evidence points to a time when there was an explosion of a huge amount of new and different animal kinds which defies the theses of common descent.