Was originally envisioned as a Prince of Persia spinoff called Prince of Persia: Assassin where you played as the Prince's bodyguard when he was a child. UbiSoft though didn't like the idea of a Prince of Persia game where you didn't play as the Prince so the game was turned into a new IP instead.
Originally, the game was to include a crossbow for ranged attacks but Ubisoft had this removed to make the game more challenging (as test gamers favored the ranged attacks over mêlée combat). Although the crossbow doesn't feature anywhere in the game play anymore, the evidence of it's existence is still in the trailer at the start up of the game - Altair is wearing it on his back along with a quiver of bolts. It was also removed due to historical inaccuracy.
As a joke, the game designers hid the image of Optimus Prime (Transformers) on certain buildings as an Easter Egg. The image appears as two boarded up windows above a triple shuttered window and can be spotted in more than one city on a number of buildings.