Allegorical Message:
I thought Into Darkness held a great a message, and was neatly wrapped off with Kirk's speech at the end of the film, about giving in to certain feelings can lead one "Into Darkness". My only complaint was I felt the message got lost at some point about 2/3 through the run.
Opening Sequence:
I have to agree that (now that I recall) this was a lot like a TOS episode feel, and I love the way the Enterprise warped off with the main musical score.
Above Average Villains:
Eh, yes and no. Cumberbatch was awesome, but he is not a good Khan, he is a good John Harrison. I always enjoy a good Peter Weller, and his character was a pleasant surprise.
Emotional Resonance:
I thought the Kirk/Pike scenes were wonderful and the same with Kirk/Spock.
Fun Factor:
Yeah this is pretty much my number one as well, it's just a fun ride that is exciting throughout. Love the effects and the variety of action, though I always want more ship on ship battles (like something out of Nemesis, one of the redeeming qualities of that film).