I've done a little studying along with my nature of curiosity to figure out a few things about the game and the sequel. As far as a location, I am partial between Asia and the Mayan civilization. Or perhaps they will explore both in AC2 and AC3 another. As brilliantly stated prior to this, on the wall is the Mayan date 13.0.0.0 which is 12/21/2012 which represents for the Mayans the last day of the world. 22:13 is a revelations chapter in the bible relating to God speaking "I am the Alpha and the Omega, the first and the last, the beginning and the end".Also stated was the Lorenz Attractor or the butterfly affect on the wall. This along with quotes such as I went into the Annymous and never returned and a few others lead me to believe Desmond no longer needs the annymous to go into the past. On the floor next to the annymous is a temple resembling that of the Mayans. There is also a building symbolizing one of japan culture next to the words Yona Guni: a island of Japan. A lot of the other messages seem to be of religion. The apple near the steps possibly symbolizing the Garden of Eden, The Eye of Providince, The Bhuddist scriptures on the wall, along with other things. There were plenty other things that can be pulled together to come to numerous conclusions.
An e-mail from Mitchell-Hedges Communications also links the storyline to Maya. In the e-mail they talk about insufficient evidnence to prove existence of the Holy Grail. Just so you know, F.A. Mitchell-Hedges is a man who claimed to have discovered a "Skull of Doom" in the Maya ruins. This could perhaps be interpreted as the Piece of Eden.
On the other hand, many hints go towards
The only other hint I got from this game that I can think of envolves Lucy. Lucy is an assassin for anyone who didn't catch her pull her ring finger back towards the end or didn't even bother talking to her during the game.
I've put all this together and here is a broad idea of what I think AC2 has in store for us:
The second piece of the AC trilogy will take place in Asia during 1300 AD...the time period in which Feudal Japan, the Koreans, and the Goths had conflict. Due to the overwhelming greatness of the importance of the mayan civilization, i believe it will be the final chapter and probably AC3. Asia brings a lot of great opportunity and might even link the assassins with the ninjas. I do believe the upcoming AC installments will have a split story line just as the first did. I don't think that Desmond will become an assassin until the third game but I do believe he will posses more abilities than before as his ancestors memory "bleeds into his brain" (as one of the e-mails to the doc suspects will happened as it did to a previous subject). The walls speak of an irreparable truth which lead me to believe that in the new games, you will try to change events so that the present day of doom does not occur. Maybe not, but still on the subject. Japan offers the same building abilities that the locations in the first game offered if not better and cooler. And for those who didn't like the cool costume upgrades in PoP probably won't be to happy about trading the assassin's dirty white robe for a kick-ass ninja one (i vote for black...maybe red).
For more on facts and discoveries in the game, check out this guys forum, he pretty much lays it out in full:
http://forums.ubi.com/eve/forums/a/tpc/f/5251069024/m/8231074016