I think it would have made a fine film, but that's not a reason to scratch Into Darkness either. Some of us enjoyed it, you know. Personally, my disappointment with it wasn't because the story wasn't all like the Nibiru sequence. I was more with the storytelling here and there. For example, I would have liked more of the attitudes of regular people after the destruction of Vulcan, like a short scene of how it affected them, and another one after the mauling of the half of San Francisco. Previous film had the mourning of the survivors from Vulcan, the new one felt like it lost an inch of empathy somewhere at the very end – or rather, it was all there, but it was there in the most busiest part where all the emotions were flowing, so it was hard to lose it. It's personal preference, I guess, but I would have picked a different kind of pause there. Like Kirk waking up in the hospital, opening a PADD and stumbling upon a video of people mourning in SF.
That would have contrasted perfectly with the opening. You started off with Kirk and Spock's to same a doomed race they knew nothing about. Then we all made that personal, with the hospital scene, switching to something we can all relate to. So somehow, making the personal bit and the mass destruction bit meet at the end in such a scene, with Vulcan's destruction also hanging in the air (there should be Vu, would have completed something that, for me, felt incomplete. Dunno, I am probably wrong.
Other than that, the storyline of both movies was fantastic. Any new films are welcome, but please don't ask for replacing them – there are other people watching.
Another note: The Nibiru sequence seemingly unrelated inclusion suggests that this is somewhat frequent for Kirk and crew. Not everyday frequent, but not something that is rare either. The new film is (hopefully) set in deep space, there are no Starfleet to go to (and at best they can come with a starship), so whatever catches up to Kirk in their routine, it will be what the next one is about. So it will be kinda like an extended Nibiru sequence...