The following article may contain spoilers, so please read with caution. I will try not to include too many things that might ruin one's enjoyment of AC2.
The ending of Assassin's Creed 1 left gamers with a sense of a larger world and story that needed exploration. With more emphasis on the story in Assassin's Creed 2, the plot only thickened from beginning to end.
Within the plot of Assassin's Creed 2, the main character, Ezio, encounters a monument of past Assassins in his Order. These assassins came from different timelines and locations. Also in Assassin's Creed 2 were pieces of Eden, some featured in the puzzles for The Truth. There were items such as a sword, a staff, etc.
With all of the different timelines and locations, the plot of Assassin's Creed 3 should be as follows.
Desmond and Lucy have escaped from the evil doctor and escape to the secluded cabin in the woods that was mentioned at the end of the game. While trying to unravel more of the mystery behind the Pieces of Eden, some big-shot corporation barges in and offers assistance to get to the bottom of it all. And since this corporation is a big-shot, they have unlimited resources to throw at Desmond, Lucy, and her team to help.
Intel comes in that there are ancient Assassin temples spread across the globe, perhaps in some of the olden Assassins locations (the ones from the monument). The corporation gives Desmond and company a cargo plane, good enough to have a mobile lab and Animus on board, allowing them to fly to the ancient tombs.
This is where the game could get really fun....
Instead of having the game take place in one large area like the two previous games (AC1 with the Holy Land and AC2 with a bit of Italy), this one would feature a city in each location around the world. Imagine this: Going to China in the modern day with Desmond, who can interact with the environment since he is now learning the abilities of the Assassins. Then he could slide into the Animus in China and go back in time to be either the famed Assassin of that time period and that location, or it could be Ezio or Altair....they could figure a method to say why he is there or how that character got to that land or time. I prefer for Desmond to somehow transform into the Chinese Assassin from the monument. Then the game could have players running around ancient China, trying to take down a Dynasty or evil warlord to gain a Piece of Eden or access the Assassin temple of that time.
The game set like this could have more interaction with the modern time of Desmond, who can now scale walls, take down armed guards, etc.
Throw in the Templars of the "future setting" or some other corporation bent to stop Desmond and you can have enemies in both universes fighting to stop the good guys from winning.
And if said Assassin in ancient China gets his tasks completed, Desmond would jet-set to the next area of the world to continue the quest. You could take him to Egypt (once again exploring modern day Egypt, the pyramids, the city, etc and then going back to the days of Cleopatra).
There are some great places the developers can take the gamers, so let us see ancient Egypt, Rome in the days of Julius Caesar, China, South America, the Mayans, etc.
It all basically boils down to Assassin's Creed 3 needing to take the plot to the next level and gameplay, giving the world as the gamer's playground. Make AC3 a globe-trotting adventure...one we will not soon forget.