This is always an important point to bring up. Why are not these separate species if they bear all the properties of what we generally recognize as separate species? As you note, if these fruit flies aren't separate species then neither are lions and tigers. So either Milton must claim that lions and tigers are the same species or admit that the fruit flies are separate species.
Similarly, I was struck by his objection to the other fruit fly experiment. He claims it wasn't shown to be speciation because it was never shown that the fruit flies are physiolgically unable to reproduce. All that was shown is that they _chose NOT_ to mate with the other group. I figure, if a fruit fly decides it ain't going to mate with a member of a different group, you aren't going to be force them to in order to find out whether they can or not. What are you going to do? Show the male a little fruit fly porn and put a blindfold on the female so they can't see who they are doing it with?
Why does he think they "chose" not to mate with members of the other group? Perhaps there was something fundamentally different about them?