I, for one, loved the design of the Vengeance. I loved the way it was filmed, how it filled up the screen. I loved seeing something that was that huge and warlike and devastating, but for once belonged to humans. And I loved the fact that we finally got a story focused on Section 31. This was what I wanted in a Trek film, and to me, it was the best film since TUC (and addresses some of the same issues). I love seeing the unsanitary things that go on behind the scenes of the Federation, that give you the utopia we all see. Star Trek throughout its history has been filled with cloak and dagger and corrupt Starfleet captains and admirals.
I have mixed feelings about the use of Khan. I just didn't buy that he was Khan. When he said "MY NAME IS KHAN" in the bridge, the first thing that went through my head was, "sure you are". I still don't really buy it on some level, for some reason. But the character was enough of a force of nature that I found myself feeling, "okay, I'm scared sh**less of you, whoever you are".
It was a great story. I suspect with a different actor, I might have bought that he really was Khan. A more charismatic, warmer actor might've brought a different quality to him. NuKhan didn't so much seem old school leader as he seemed weapon in human form.
HOWEVER - I also feel that in this day and age, this is exactly how Khan would've been written.
Nonetheless, you really can't escape the fact that the character of Khan comes with fifty years of lore baggage.
But on the whole, this stands out as one of my very favorite Trek films.