Desmond and with him the modern setting make the game so much better on a story level.
Working together with DaVinci is cool and finding the Apple of Eden as well, but the story of Ezio and Altair are not nearly as interesting when there is no real connection.
I was always incredibly excited when I finally beat an episode and could return as Desmond and gather more information about the whole consipracy and Subject 16. Finding out that Lucy was in fact a modern Assassin etc.







