There's five keys to the door that locks Alta´r'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 Alta´r were this before dying), and as seen in AC 1, Al Mualim (the Grand Master) wore black robes, rather than the common white robes, and Alta´r's Armor in AC 2 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 Alta´r'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 Altair
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.
Alta´r 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 Alta´r's accented Italian. In Assassin's Creed I, Alta´r is speaking and translating from his native language and hears no accent himself. It could also be that these memories of Alta´r are being viewed from a different Animus: Abstergo's Animus channeled Alta´r'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.
Alta´r sounded Semitic to me.
In AC 1, AC 2 and ACB, Alta´r, 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 (Altair, Ezio, and Desmond) have had much more experience with the ability, so they're able to use it better.
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 the first game, Vidic noted that "we already have the Masyaf artifact." But we see in Revelations that Altair 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.
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.