There's no question that City on the Edge of Forever is the best episode of the original Star Trek series. The top five is open to some debate, likely including Amok Time, The Trouble with Tribbles, and Journey to Babel. But for me, the clear #2 is Space Seed. The tone is darker, less optimistic, more wrought with tension. The stakes feel higher. This is almost entirely due to the presence of Khan Noonien Singh, Kirk's great antagonist. Ricardo Montalban's simmering, combustible performance brings out the best in Shatner, both in this remarkable episode and fifteen years later in the second feature Trek film, still the best big-screen installment of the franchise.
Khan is a product of superior genetics, a relic of the Eugenics Wars from late 20th century Earth. As such, he represented an allegorical commentary on the arrogance of science in our own times, a frequent device employed by writers on the original Trek. The augments, as Khan and his followers came to be called, were the triumph of genetics and the failure of ethics. They were physically and intellectually superhuman, but their ambitions and lusts were unfettered by human empathy and compassion. Khan in particular so lacked humility that he fatally underestimated the human capacity for self-sacrifice. Twice.
The scenes between Khan and Kirk are some of the best science fiction, heck, any fiction, have to offer. In Wrath of Khan, the screen crackles with the electricity between the two. Their shared story is one of vengeance, creeping mortality, and loss. In the end, as everything collapses around him, Khan realizes that he has failed, and it has cost him everything. But there is no redemption, no great epiphany. There is only the durability of hatred, and Khan clings to it at the last, quoting Melville: "From Hell's heart, I stab at thee... for hate's sake, I spit my last breath at thee..."
I do not recognize the recent films calling themselves Star Trek. I do not comment on high budget fan fiction.