The story (and game) definitely isn't for everybody.
I think they put far more emphasis on the game's engine and graphics (to this day no other game looks nearly as "life-like" or "photo-realistic" as Crysis) than the plot.
However, this game and engine has proven that it'll last a long time and as such the sequel is sounding to have far greater depth- which will be welcome. Graphics, however, are likely to be very comparable to the first one- which is more than awesome by me. The big difference, however, is Crytek is stepping away from the jungle and moving more towards the city.
My favorite part of the game had to be while on the carrier- I felt that part was just *way* too short.