Just finished the game, I think it's the best I've played this year along with Uncharted 2.
The story is quite fascinating and for once it seems it was all planned since the beginning of the series so they really have a whole story to tell, they're not just adding crap to continue on making games.
So basically from what I've understood, there was an ancient race of 'gods' on the earth before humanity existed. They created humans and they co-lived in peace for a certain period. Humans were created to obey to these 'gods', pieces of Eden are the tools which the 'gods' used to control humans (in the game there is this theory that humans have special neuro-cells which respond only to the fruits of Eden).
But Adam and Eve stole a fruit of Eden and freed humanity from the gods' control. A war started but while both 'gods' and humans' were busy fighting each other a natural catostrophe happened and a huge sun flare almost erased all life from earth.
But both gods and humans managed to survive and rebuild the world. The gods left a warning to future generations about a new incoming castrophe destined to happen 'in present day'. That message seems to be intentionally destined to Desmond, with Ezio one of his ancestors being a prophet/tool.
At this point it's clear that the main problem isn't about the templars and their will to control humans using the eden's artifacts (like it seemed it was the case at the end of the first game) but to prevent a new catostrophe. The game clearly hints that this catostrophe is related to the Mayan 12 21 2012 end of the world theory which might happen through the reversal of geomagnetic field.
Desmond must finds these temples built at the time of the first catastrophe to protect gods/humans from the fire to possibly save the world again.
Now of course the story has left me with a few questions. These 'gods' don't seem to be aliens at all (sorry UFO fans
), they're clearly intended to be linked to the ancient roman/greek mythology type of god. It's not clear if these gods are now dead or if they have left the planet by present day (or if they have left the plaent in the sense they're dead). But more importantly if they can see the future, if they can see that Desmond will end up looking at his genetic memories and find about Ezio and the prophecy they left to him, it means that everything was predestined to happen even them leaving a prophecy, that they can very well see how everything's going to end, so in this sense, they're guiding Desmond to what is already destined to happen in the future too.
The usual doubts/inconsistencies related to time travel stories btw
Btw I think that with the inevitable AC3 they should cover the french revolution and the following napoleonic empire era.