Well, I'm going to start calling him the Man In Black SMOKE, since he's the smoke monster (which is why they were giving us hints at the end of season 5 by dressing him in black).
I assumed Richard said "YOU!" merely because he finally figured out who he was. And I'm guessing he hadn't seen him for whatever reason he also hadn't seen Jacob in person all that time. Plus, it seems the Man In Black has been cloaking himself as the Smoke Monster off and on throughout the decades... and Richard might have had a hard time recognizing him for that reason too.
It's like everyone suddenly realized that Jacob being dead ipso facto meant that the Man In Black was now in charge.