Well they were originally going to have eyehounds and squidbulls in Half Life 2, so I don't think that consider them wiped out, and those alien sharks are still here.
Well he clearly has access to a lot of theoretical physics shit so clearly he has something to do with either Black Mesa or Aperture Science. How else is he like a God Man? Oh wait, that's another possibility. He could be God :p
Do you think Episode 3 will feature creatures from Half Life 1/Opposing Force that weren't in Half Life 2? I loved Half Life 2, but personally I thought the original was better since it had more variety with monsters. Antlions were fun to fight, but only for a bit, I miss fighting...