That inherent insecurity of the franchise, from the biggest top executive down to the tiniest fan, is funny at times.
That's how you get mediocre films. Star Trek Into Darkness was a clear in your face attempt to cash in on the Dark Knight vibe, just as Star Trek Begins was an attempt to cash in on the Star Wars prequels and Batman Begins. Everyone of the involved told you that this was what they were aiming at. It didn't came to them organically, it wasn't an idea they genuinely liked, it was an idea that they thought was dictated by the market.
They forget that the original films they were "inspired by" didn't do that. The Dark Knight is a genuine film through and through, and you notice that in every aspect of its execution (with The Dark Knight Rises on the other hand, you already notice that a lot of that got lost and they did try to make a second TDK).
And that's also why they are disappointed, studios and fans alike, with the box office that is actually okay. So this film didn't became their Dark Knight or their Skyfall? Well, too bad. Don't expect your films to perform better than average just because you imitate the extremely successful ones.