Renegades and antithesis
I had precisely the same thought upon seeing the "Into Darkness" trailer: the plot appears to be a sci-fi remake of "Skyfall," which itself recycled the very similar plot of an earlier Bond film, "Goldeneye." Each appears to be about a renegade agent coming back to battle the hero and his generally virtuous organization, which he accuses of duplicity or hypocrisy.
It seems like a somewhat paint-by-numbers way to confront the hero with his antithesis, a dark mirror image that the audience will immediately accept as his greatest challenge. It's a popular plot structure because it instantly sets high stakes for the adventure, in a way that can be easily communicated to the audience through short clips and posters. The villain has all of our hero's strengths - but he's evil. Or maybe he's not so evil, and he will subject the hero to a searing crisis of ethics, a test of personality. Our hero will suffer both mentally and physically, as he has never suffered before!
Who doesn't want to buy a ticket to see that?
It's not an entirely new idea for Star Trek, because even the original series had a couple of episodes featuring starship captains gone bad. The very best episode of the uneven latter-day series Voyager, hands down, was the two-part episode pitting the crew of that lost Federation ship against another lost Federation ship, whose desperate captain and crew had made the kind of mistakes Our Heroes managed to avoid. Particularly when the good guys are as good as the utopian Federation, it's an appealing route for writers to take. What more terrible challenge could they face than an attack on their noble moral code? You can't beat that by re-modulating the deflector shields.
There's no reason we can't also have the sense of wonder and discovery that illuminated Star Trek, but I have the nagging fear that every Trek director is going to spend the rest of Hollywood history trying to remake The Wrath of Khan, which means you need a colorful bad guy and lots of revenge. We already got that in the first J. J. Abrams Trek film, didn't we?