Cesare's insistance that "No man can murder him!", is a lot funnier when you remember that Assassins are not mere men.
Back in AC2, when Ezio is escorting Claudia and his mother to the villa, Claudia asks a series of questions ending with "Did they [their family] get a proper burial?" and Ezio answers "Yes,... they did." At the time most players assume he was lying to comfort her (and the novelization had him sending the bodies down the Arno River in a burning boat), but in this game we see at the end of the second Cristina Memory that the bodies were indeed buried.
In Assassin's Creed I, Al Mualim states that he has faced a thousand men stronger than Alta´r and has defeated them all and he uses the Apple of Eden. Alta´r then proceeds to defeat him with relative ease. It's revealed in Assassin's Creed: Brotherhood that the Apple of Eden's illusions are Cast from Hit Points, which might explain how Alta´r managed to defeat Al Mualim. It's possible that he was talking out of his ass, but the former is more likely.
Revelations, on the other hand, shows Alta´r wielding the Apple with no such difficulty, slaughtering hordes of attacking Mongols with no trouble at all. It seems more likely that Eio's difficulties in wielding the Apple stem from his inexperience at using it. Al Mualim had spent weeks in possession of the Apple, studying it and understanding it. So yeah, he was probably talking out of his ass.
Assassin's Creed III, ON THE OTHER HAND, shows something that's absolute Fridge Horror: the Pieces of Eden are all like the One Ring, subtly manipulating and brainwashing those who come in contact with them. For all we know, NOTHING Altair remembers is exactly what happened. Al Mualim's corruption could have been either the Apple's manipulation or an illusion. So could have been his defeat at Altair's hands. It would also explain why Cesare and his fellow Templars suddenly became inefficient and incompetent after attacking the Villa. Machiavelli made a huge speech on Cesare's The Dreaded and Bad Ass status, but by the time Ezio reaches Rome, they're all acting off, with Rodrigo hiding the Apple rather than using it to consolidate power.
Claudia's skill with a knife shouldn't really be all that surprising. She's spent twenty years surrounded by mercenaries, with a fighting ring right outside the front door of the villa, and nothing else to do — something she explicitly complains about in ACII. Add in memories of the ugly fate of her father and brothers, and she'd have a damned good reason to learn how to fight and plenty of time to develop those skills with the help of Mario's mercenari.
Often times, while free running on buildings, a citizen may ask "isn't that illegal?" When you go up on rooftops with Borgia up there, they attack you as soon as they see you.
They also attack thieves who also free run.
Lucy explains at one point that she's getting most of her access to Abstergo's files through old passwords and the like. It's no stretch of the imagination for some important people at a megacorp to be embarrassingly bad at password security, but if you recall from the first game that Dr. Vidic is kind of a living security flaw, she might be getting all the remote access that's gonna exist....
Actually it just turns out she's a Templar double agent and is probably being given all that info as part of their plan.
The You ALL Look Familiar in Brotherhood multiplayer is for Paranoia Fuel. All the NPCs look like PCs... How do you tell which ones are which? Newbies will give themselves away with High Profile actions, but you will never see an expert who's blended into the crowd unti-*SNICKT*
It always bothered me that Bonfire of the Vanities and Battle of Forli were broken memories in AC2. Then, while playing Brotherhood, it was revealed that Ezio had repressed most of his memories of Cristina Vespucci, who only appeared once in AC2 to have sex with Ezio. Not only that, but Cristina died during Bonfire of the Vanities. Since Savonarola was present during both of the broken memories, Ezio associates him with her death, and has been trying to block out EVERYTHING that reminded him of Cristina as anything more than another conquest. It was a coping mechanism.
Why did Desmond claim his mock Italian accent in Brotherhood wasn't racist? Because he's descended from Ezio, so technically, he is Italian! He was making fun of Alta´r at the time, but that also doesn't count as offensive against Syrians because he's also descended from him!
Might also have been stuck in his head from II when Mario introduced himself with "It's a-me! Mario!"
One of the e-mails from Vidics computer in the first game is written by an insane person in ALLCAPS about how he saw people with the Abstergo logo using a metallic ball that made everyone kill each other. The first game actually hinted at the finale of Brotherhood with Ezio using the piece of Eden as a weapon.
The Cristina memories are started at different locations in Rome, where the player sees Cristina...or at least someone who looks like her. These are probably actually locations where Ezio saw a woman who reminded him of Cristina in some way.
Why is Ezio's hideout on Tiber Island and not anywhere else in Rome? Historically, the island has been associated with Asclepius, the Roman god of healing, with a temple dedicated to him there, and the island had a hospital built there in the Renaissance. Ezio's purpose in Rome is to liberate it from Borgia depredation and helps to restore the city to its former glory. In essence, the Borgia are the sickness, and Ezio is the cure.