There remains doubt over the status of Songhay, Hatsa, Sandawe and a few other languages, but what is remarkable is that in the last 30 years there has been so little major revision. No one has proposed fewer groupings. Bender has separated Western Cushitic off from Cushitic as another branch of Afroasiatic that he calls Omotic. Greenberg's work is, contrary to what Peter Daniels says, not about subgrouping but about large families. As for eye, from the top of my head, the cognate set exists in both Semitic Arabic and Cushitic Somali as, respectively, Eyn and Il.
Semitic languages are a minority numerically in the group.
Semites emigrated from the African side of the Red sea anyway and exported an African language to Asia where they met Asians such as the Persians, Assyrians and others. This is the only logical way to account for the presence of an African branch in a place where it is surrounded by unrelated languages. It would make sense to change the name of the group to something like Ethiopic or Ethio-Chadic. In a later publication, viz. The first important contribution of Greemberg's classification scheme was that the given groups were related into a larger family.