The story didn't go over anyone's head, it simply wasn't told properly. Or at all in some cases. It was brutal, and I wanted to appreciate the story but it just wasn't there. Gould was insufferable, Lockhart was imbecilic, and Hargreave was beyond asinine. These were bad roles, with poor writing and sub-par voice acting. And the over arching story was just plain dull, probably because it was never told properly.
I had the same problem with the Halo sequels, they seem to expect you to read a damn book to understand what's going on with the storyline. This is unacceptable, the books can "fill in the holes" for fans that are into it, but games are games to me... I read plenty enough as it is and I have no interest in reading a book about a game.
With all that said, I really liked Crysis 2. Graphics were solid but with poor texture work in a lot of places, hopefully the new patch fixed that. The DX11 effects look snazzy. The gameplay was fun as hell, super intense firefights and fun locales to have them in. Verticality in map design is something they learned from some of the later Crysis Wars downloadable maps, this was on full display in Crysis 2 as well. Overall I really liked it and will play through it again on a harder difficulty as soon as TF2 releases it's new found grip on me.