I really do think JK lacked in terms of story and athmosphere. Again, I cannot stress enough how much I enjoyed the game, but some parts of it could've been cleary made much better.
I would have enjoyed some more civilians. (Maybe at least some who would run away screaming once you or some stormies appear.)
I liked the appearance of the second reborn in the Freezing chamber, that had a great athmosphere, but that was one of the few really climatic scenes.
Besides, the scripting in the cut-scenes has some problems with unforseen events. (Like me placing 5 automatic guns in the room where Galak shows up, man, that cut-scene was really messed up) I was kinda dissapointed by that. Not to meantion the fact that you cannot ABORT the scenes! (Seeing them once is okay, twice, yes, but anything mosre than that just plainly sucks)