Okay so the Templar Awareness mechanic is a little convoluted but kind of makes sense... except for one part: Stalkers. If you counter a Stalker, the awareness takes a big drop, usually enough to drop it to 0 in normal gameplay. But if you get stabbed by him... the awareness level increases. What makes this fridge logic and not just normal video game logic? Since this is how much the Templars are aware of your actions, this means that they expect that Ezio Auditore could be stabbed by a random sellsword... but countering that? No way Ezio could counter an attack.
There's five keys to the door that locks Altaïr's library underneath Masyaf, but way more keyholes than that. The door is drawn or etched with a few animals from the Western zodiac, and all five of the "correct" keyholes are on the same constellation: ''Aquila'', the Eagle.
In Revelations, Desmond is suddenly wearing a black hoodie, rather than his white hoodie. This might not just be because he's inside the Animus and in a very depressed, mentally broken state, but possibly also because he's now been trained and has the same skills as an Assassin Grand Master (both Ezio and Altaïr were this before dying), and as seen in AC1, Al Mualim (the Grand Master) wore black robes, rather than the common white robes, and Altaïr's Armor in AC2 has the same black color. In other words, the Animus shows us that Desmond is now as skilled as an Assassin Grand Master, and not just a student any more.
Furthermore, notice the color of Ezio's clothes during his trip to Constantinople. They're dark gray/black, just like Al Mualim's robes and Altaïr's Armor.
Suleiman and Ezio become quite suspicious of a certain man and wind up executing him, only to find out a bit too late that he wasn't necessarily against them. This is the sort of thing that happened a bunch of times in Real Life's Suleiman's life, including with one of his own sons.
Since Subject 16 wrote the database entries for Revelations, it might seem a bit inappropriate when he gushes over how hot he thinks Sofia is, what with her being his great-great grandma. But when you factor in that he's spent at least as much time as Ezio as Desmond has, his confused feelings are a bit more explainable.
Considering Subject 16 says both that he and Desmond are cousins and he had less time with Ezio than Desmond it might be more likely that he's descended from one of Ezio's many illegitimate children from earlier in his life than Sofia's children.
Word of God says Clay was descended from one of Ezio's illegitimate children, so he wasn't actually gushing over his grandmother there.
Remember the identical grandson thing? Now is it just me or does Darim look just a little bit like Subject 16?
Clay is descended from Ezio, who is NOT a descendant of Altaïr.
Why did Selim banish Ezio? Because Selim likely wants to keep the city safe, and considering Ezio was causing a war in Constantinopoli with the Templars, Selim wouldn't want to get caught in the middle of this.
Altaïr develops an accent between the first game and this one. Since the game is being played from Ezio's point of view, he hears and translates Altaïr's accented Italian. In Assassin's Creed I, Altaïr is speaking and translating from his native language and hears no accent himself. It could also be that these memories of Altaïr are being viewed from a different Animus: Abstergo's Animus channeled Altaïr's voice with an American accent to make him seem more acceptable to the user and thus help with synchronization. The Assassins' Animus, on the other hand, translates with native accents as, Lampshaded by the second game, the Animus 2.0 has issues with translation. As late as Revelations, the Animus 2.03 only mostly but doesn't completely translate, although this crops up more with Turkish than Italian.
Altaïr sounded Semitic to me.
In AC1, AC2, and ACB, Altaïr, Ezio, and Desmond have an ability called Eagle Vision. In Revelations, it is renamed and upgraded to Eagle Sense. This may not sound so much like Fridge Brilliance, but in the final sequence with Desmond in Brotherhood, we are told by Those Who Came Before, that they created us humans to be like them, but kept one of their six senses from us, and later in the same sequence, Desmond is told to "Awaken the sixth". There is no reason for Ubisoft to change and upgrade Eagle Vision all of a sudden, unless it's because the sixth sense kept from humans by Those Who Came Before is actually Eagle Sense, and the Eagle Vision is a more limited version of the Sixth Sense. Besides that, Desmond at one point states it feels like he has a kind of sixth sense.
Plus, by that time all three characters (Altaïr, Ezio, and Desmond) have had much more experience with the ability, so they're able to use it better.
Brotherhood described the sixth sense as "Knowledge" (as in, Sight grants seeing and Knowledge grants knowing). Eagle Sense allows the characters able of it to instantly tell who is hostile, friendly or neutral, find useful objects and places and - in Revelations - to even know walk routes without even having seen once who walked them. Almost as if the characters just know about the world.
In The Lost Archives, we learn everything about Clay, and especially why he appeared so abrasive towards Desmond in Revelations and, most importantly, why he was so rude about Lucy. Through Juno Clay learns that Desmond is The Chosen One, and isn't happy to find that his hard work was for nothing—that he's just a pawn in a greater scheme. So he finally meets Desmond, the guy he was, in a sense, destined to help, stuck in a similar predicament as Clay was. As for his hatred toward Lucy? She was supposed to get Clay out, but she betrayed him. His father is all alone now because she kept him in Abstergo, and he hates that Desmond doesn't know this and is having a Heroic BSoD over a woman who was going to betray him to the Templars.
Why does your Templar Awareness go up with most actions (such as renovating), in contrast to previous games? Probably because the Stalker soldiers, the ones who can blend in with the crowd,are watching your every move and reporting back.
In Brotherhood, the existence of an Assassin in Rome was known since the Pope himself was in on it. What the assassins did was only hubris on the side. Constantinopel on the other hand is split between the Templars, Assassins and Ottomans, with the Assassins having worked from the shadows before Ezio's appearance. So when someone suddenly starts owning entire city parts, chances are Ezio is making the Templar's not exactly aware of his existence, but of where he is (thus leading to the den attacks). Plus, since also the Ottomans join in with getting suspicious once full Templar alert is activated, chances are that a foreigner buying like 50 businesses is mighty scary to the population (see the Heralds and their fear-mongering).
How come there are no wanted posters in order to lower your notoriety? Because the Ottoman Empire is Islamic and the depiction of living beings in art is strongly discouraged in Islam.
Clay's As You Know to Desmond is helpful to new players, but really egregious to anyone familiar with previous games - however, there are several reasons for why. First, Desmond is currently in an Animus coma, and that could have wrecked havoc with his mind, including memory. Second, Clay is the middle of severe Animus schizophrenia, so he needs something to help anchor him to the here and now as much as possible. So Clay is going with a just-in-case-he-did-forget mentality, even if it ultimately wasn't necessary.
In the first game, Vidic noted that "we already have the Masyaf artifact." But we see in Revelations that Altaïr locked it away in his library vault, specifically saying "it needs to be hidden until its secret has been passed on." How did they get it? Ezio refuses to pick it up, noting that if he does, his quiet life with Sofia would be in jeopardy. The Templars just kept trying to go after it, and eventually succeeded.
Also luckily its secret had already been passed on the moment Ezio came into contact with it thanks to a twist on You Already Changed the Past, so aside from its run of the mill Mind Rape powers, it was essentially useless to the Assassins.
Of course, once you play Assassin's Creed III, you realize Ezio might have abandoned it and chosen to leave the Assassins because the Apple brainwashed him to. Why? So that it could wind up in the hand of the Templars, and then blow up and cause the web of events that would lead to Desmond freeing Juno. Ezio's Happy Ending came at the price of his descendant dying, and probably the end of his lineage(Desmond had no children, and his father has no other sons or daughters that we know of). Oh, and the Templars get Desmond's body, which allows them to learn all of Ezio's secrets.
Desmond has a son as of Syndicate.
The Lost Archives takes you from Animus Island, to a runthrough of Subject 16's life up to this point. At the end of memory 7, "The End of The Line", you are deposited back on Animus island, and when you go through the gate like you did at the beginning of the DLC, it sends you back to memory 1: "The End is the Beginning". How many times has Clay gone through these memories, only to fail at the very end and restart?
Look closely at the last archway Clay could never reach. It's the Animus loading room beyond that archway—it's the way out. But he has no body anymore, and the Animus knows this. So the bridge collapses and he falls, putting him back in the beginning because the Animus knows he's still there and its trying to get him out. But there is no out. He's at a dead end. It wasn't so much as failing as he can't get out because the Animus doesn't see his body there for him to reach. This loop is probably what Clay was doing to keep the Animus distracted from deleting the excess data (which was Desmond). We have two disembodied minds in the Animus, and the Animus doesn't know what to do with them. The system is going to crash, but its priority seems to be getting Clay back to his body, which it will try to keep doing, until the very end when the Animus realizes that it doesn't need all this extra data and should just dump them to get back to working order.
Oh, that's not nothing. How about killing the peaceful but Templar Ottoman Prince and then leave his psychotic, warmongering brother and his Knight TemplarPraetorian Guard Janissaries in charge? Despite the fact he promised Suleiman he'd try not killing Ahmet. And since the Assassins have an agreement with the Ottoman Empire, chances are they'll sit back while Selim murders thousands, just because he isn't a Templar.
It is primarily these facts, coupled with most of Ezio's actual assassination targets in AC2 apparently not being Templars, just political rivals of the Medici, has led this troper to the conclusion that Ezio isn't as perfect as his fans would like to believe. Assassin's Creed III and its protagonist are criticized for having the player kill British soldiers, who are also stated to not be Templars for the most part, but most of those situations where you the player kill them are not necessarily canon. The assassination missions from Lorenzo, leaving Selim in power, killing the leader of the Janissaries who was not actually plotting against the Sultan, and killing who knows how many innocent Byzantine civilians...these all happened, and Ezio canonically did all of these of his own free will, and in some cases they were his idea. Suddenly everyone's favorite Assassin is looking an awful lot like a war criminal.
It's an overarching aspect of the series; these two have been caught in a Forever War, and thus anything Assassin/Templar is inherently worse to the opposite site than non-aligned, at least subconsciously. But that aside, these two primarily fight for control behind-the-scenes, rather than every conflict that exists, because those are the deciding victories to them; if they think it'll work for them in the long run, such compromises as the above examples can be tolerated 'enough', at the very least.