Yeah, "Emissary" is one of my most re-watched episodes and the best Trek pilot for all of the reasons given in this thread. Only "The Cage" comes close to beating it when comparing the other pilots.
Ben's struggle just pulls you in from the start. It was smart of the writers to show us how he lost Jennifer. Those scenes were some of the most powerful in all of Trek. And the moment when he breaks down and realizes that he can't let go of her was some of Avery Brooks' best acting.