It does a little bit. I wouldn't say the idea is the same. We still have no idea what the deal is with the aliens in Crysis. And thusfar, there is no conspiracy anywhere near the level of Half-Life (i.e. G-Man and his "employer").
Yes I noticed that, too, but it's no bad sign. Crysis 2 story is still more about the Nanosuit and it's wearer, so that there are still enough differences.