This is speculation on my part but I think a major reason for the specific time period was its familiarity with most people. While egypt during its "prime" would have been interesting I think the time period kinda made the exploration more interesting since you had the chance of exploring places that might not yet have been built during the previous era. Also this specific time period offers players more variety when it comes to towns that they can visit in the game. So the player can explore Alexandria with its Greek architecture and then visit Memphis where Greek influences in building styles are not so heavily emphasized.
The only thing I kinda dont like is the fact that having this be an origin story kinda limits the chances of getting an assassins creed game set in ancient babylon or in China during the time period when the first emperor of China lived.