The second time for me was better, trying to wrap my head around it after the first viewing made me realize that 90% of the story occurs off screen.
All we see on screen is; mission at the beginning, loss of command, attack on hq, warp to Kronos and get Khan, race home without dying. When you think about it alot of the story has already occured off screen. Marcus has a plan to start a war Cheney style and it has a little to do with Vulcan's fate, Khan de-rails that plan a bit, but Marcus is able to make it work to his benefit.
Then the movie starts, and Kirk and Co mess up Marcus's plan even more. Its really not that much and alot of what I thought were plot holes after the first time, were explained in an offline at the beginning or end of a scene.
I think Spock yelling Khan was not silly after thinking about what old Spock would've said to young Spock concerning how they defeated him. Of course old Spock told them that one of them had to sacrifice themselves to survive. NuSpock yelled Khan because in just acting to save the ship there was no way around it here either, one of them had to sacrifice themselves...and at that point Khan still wasn't defeated. The first time I saw it, it seemed cheesy but on the second time it did not.
My wife made a comment, I know its not applicable but I thought it was cute. Shes not fully up on the alternate reality thing, she still in some ways thinks its a reboot and with some of the stuff we see shes right. But when the tribble came back to life she stated, "Ahh, so that's how they multiple so quickly...Khan's blood's regenerating powers!" I just said yeah probably, but I though it was cool.