Omotic, a small group of non-Cushitic, non-Semitic languages spoken in the highlands of Ethiopia, has always been the odd one out in Afroasiatic; by anyone's tree it is the first to have split off, and the noted Chadicist Paul Newman expressed scepticism about its membership in the family. I know little about Omotic, or Cushitic for that matter, but after reading a few sketch grammars in Omotic Language Studies , I found it very difficult to imagine these languages as Afro-Asiatic; with Berber or Hausa or Beja or Semitic the cognates are instantly visible, but none of the most familiar grammatical morphemes or lexical items seemed to be present. However, a paper I just came across by Rolf Theil is the first I've seen to present an argument against the hypothesis, and a pretty good one at that. There are parts I would question - for example, the suggestion that pronouns are unreliable (they are conspicuously unreliable in regions where extensive politeness systems have developed, like East and Southeast Asia, but I didn't think highland Ethiopia fell in that category) - but the overall argumentation seems good. In particular, the attempt to show that a roughly equal number of similarities can be observed between Omotic and families other than Afro-Asiatic is on the right track - if Omotic were to have more similarities with Afro-Asiatic than with any other family, then merely pointing out problems with some of those similarities would be inadequate. I'll be interested to see the reactions of people better acquainted with the family.
On another note, I passed my upgrade presentation yesterday - yay!