The modern day story part of this game seems incoherent to me. (Spoilers)

(If you have not yet played the third Desmond mission, do not even read this. Spoilers.)

While I was going back to Abstergo as Desmond to rescue his father, I remembered how, in Assassin's Creed 1, an Assassin team supposedly tried to rescue Desmond. You heard gunfire and alarms and the team ultimately fails. So, when I just waltzed into Abstergo and single-handledly killed dozens of security guards with a hidden blade, I thought it was pretty contradictory. And when the guards are supposedly "authorized to emply lethal force" by Vidic, it does not get any harder at all. So, this implies that an entire Assassin Team, well equipped (it is made evident by the gunfire that you heard in AC1 that they have firearms) and well prepared cannot even make past the entrance of Abstergo Industries, but a single man who is at first only armed with an outdated blade can? 

That really disappointed me. Throughout Assassin's Creed 2 and Brotherhood, if you read the emails, you kinda felt that the Assassin Order was helpless and that they DO have reasons to keep low profiles. This game, however, invalidates that feeling.