But mainly, the story would be quite broken if there was no transition and it just said "6 months later" or something lame of that type. Prophet had mysteriously rigged the alien weapon, then taken a VTOL back to the island at the end of Crysis, with Nomad, Psycho, and Helena going after him. In my opinion that is not a good way to tie off a story if there isn't going to be an epic final battle on the island.
The best storylines I have ever played are from Mass Effect and Mass Effect 2. Both had countless twists and drama throughout the story, but at the end of their storylines, they tied off most of the story with a solid ending, although not completely, in order for the next title of the series to connect the story.
Crysis did not have a solid ending in my opinion, the carrier was destroyed and Nomad and the rest of the team are headed back to the island after Prophet. I remember Crytek admitting that the ending point of the Crysis storyline was originally supposed to be the halfway point in the story, but was made to be the actual ending due to time restraint. And that says it right there, not only is it a cheesy ending, it wasn't even supposed to be the ending in the first place.
But with all the delays of release and possible leftover work from Crysis and Crysis Warhead, I hope this time Crytek can finish the story where it was orginally intended, and maybe win a few game of the year awards with Crysis 2, don't you think?