Even though Obi-Wan is fully aware that Anakin is not the person he once knew anymore, i think this is the moment he can really see all the hate in his former padawan’s eyes. This is the first time he truly sees Vader and he is scared. It is the first time he can really see the dark side of the force. He realizes that he is not facing Anakin here, he is facing the dark side. Obi-Wan faced it once before when he faught Darth Maul. But this time it’s different. This time the dark side is wearing the face of his brother. Anakin is now merely a vessel to the dark side of the force, an empty shell. Everything Anakin once was is either being repressed or is fully gone. Obi-Wan tried to figure out what it is during the fight and now he is convinced that it is the latter. Here he experiences first hand what the dark side does to a person and he is not only scared, he is terrified.