But we've had that since "Pen Pals".
That's not the same thing at all.
Kirk and Spock were always super-heroes.
I feel like they were just plain heroes. Most superheroes have some great origin story as to how they got their powers or why they wear their costumes. Spock was just born the way he is like many other Vulcans, and they were just a few of many individuals in a military organization. That's not really that super.
Once an element of destiny was introduced to add some excitement, that's when they became superheroes. Suddenly now they are agents of fate with a destined purpose. Kirk is destined to be the Captain of the Enterprise, and certain elements of the crew are destined to be together. None of that was present before, that's just one of their changes to the Star Trek universe. And they're entitled to do that.