Al Mualim spends quite a bit of time explaining to Altaïr about how he needs to "pierce the illusion" and how Assassins are trained to be highly perceptive, and how their creed is intended to make them wise and see the truth in all things. The real significance of this is that Al Mualim was specifically talking about Eagle Vision, and how Altaïr uses Eagle Vision to literally pierce the illusions created by the Piece of Eden.
We tropers have turned Altaïr into a Memetic Badass, and while most of that is based on the game's attempt at justifying Regenerating Health, not all of it is. To wit, the synch bar's length increases as Desmond grows closer to Altaïr, by doing things Altaïr remembers doing. However, the synch bar does not increase when Desmond kills one of the sixty Templars. He can kill every Templar in the game without increasing the synch bar in the slightest. In other words, Altaïr may have killed every single Templar in the Holy Land, and he doesn't even remember it. Just another day at the office.
There is an unflattering legend about the real Assassin Order that says that the members of the order indoctrinated promising young men into becoming assassins by taking them to a beautiful garden while they were under the effects of hallucinogenic drugs and then telling them that what they had just witnessed was Paradise itself, and that they could go live there one day if they did exactly what their mentors told them to. Apparently, that was the source of their suicidal dedication to the order. In-game, behind Masyaf castle there is a beautiful garden, which is also where the final boss fight takes place.
If you look at the memory log for the last mission, you'll notice that garden is actually called Paradise. Al Mualim also references this legend when you talk to him after Garnier's death.
You also see a hint of this at the very very very beginning of the game, when they try to drop Desmond at the last memory and it starts rejecting him. Altaïr is clearly in that garden and a group of (faceless) maidens are flocking around him. This is a Mythology Gag. The legend is mentioned in-game, and makes it clear that it's completely false. In fact, Altaïr considers it an embarrassment.
In the first game Altaïr the only character in the animus who doesn't have an appropriate accent. It's not Desmond's voice, but it's not, it's a completely different voice actor. Why bother getting an American accent for Altair when everything else was made as historically accurate as possible? It's Desmond's voice AS HE IMAGINES IT SOUNDS. To Desmond, his voice sounds more badass than it actually is, so when in the Animus, he naturally has a cooler sounding voice.
The game was boringly repetitive for a reason. The designers wanted to show that no matter how cool a job may seem, it's still a dull routine after you keep doing it, day in and day out. A warning to people considering a potentially "cool" or "fun" career, demonstrating that even something as interesting as assassinations loses its entertainment value after seven or eight times.
Acre seems to be the worst off out of all the cities you visit, especially its poor district. Whole buildings have been damaged or completely destroyed. It is also the only city where you see dead bodies that were not killed by Altaïr. This is damage resulting from the siege of Acre (in-game dialogue suggests that the game takes place in August 1191). Look at the approach to the city and you can see the remnants of siege machines surrounding it. The Poor district is nearest the gates, hence all the wrecked buildings that have had trebuchet boulders thrown through them.
If you take too long in the battle against Al Mualim, he'll use an unvoidable attack to blind you. When this happens, you automatically begin to desynchronize. If that's the case, then that means Altaïr never got blinded. Curb-stomping Al Mualim with a counter from the hidden blade is what actually happened!
Considering the placement of all the major locations—Masyaf, Damascus, Jerusalem, Acre, and Arsuf—then the Kingdom must be mostly in Lebanon and northern Israel.
Just an extension of the Animus/genetic memory train of thought. Why are Acre, Jerusalem, Masyaf and Damascus apparently just a few minutes' horseback ride away from each other? Because all that Altaïr remembers from their vicinities are the landmarks saying that he's getting close to his destination, as well as other signs reminding him that he's leaving a certain city. The rest of the realistically days-long journey is promptly forgotten — erased from his memories. Therefore, Desmond's experience with the geography is just those places more familiar to Altaïr stitched together to make them appear seamless.
A bit of Fridge Horror. We are revealed in the ending that Al Mualim is a Templar, and has apparently been for some time, but we are given no further explanation. There's no Freudian Excuse, no Dark and Troubled Past, not even a recollection of when and how Al Mualim joined the Templars. It's just something Robert says and it's confirmed when Altaïr goes back to Masyaf. However, for those who played Assassin's Creed: Revelations and Assassin's Creed III, may realize the truth: Al Mualim was being controlled by Juno through the Apple. The Pieces of Eden are sentient, and anyone who comes in contact with them is also put under their control, however unconsciously. Al Mualim claimed the Apple couldn't control Altaïr, but that's because Juno needed him to continue her plan. Now, why Robert de Sable would claim Al Mualim is a Templar? Because he might have not touched the Apple, but he was in Solomon's Temple when Malik took it (which, by the way, is never explained HOW he escaped, but more of that below); it's entirely possible the Apple programmed Robert to tell it to Altair as his Famous Last Words, while it brainwashed Al Mualim to become what it wanted him to be. So, in reality, Altair was Juno's Unwitting Pawn, and he killed his innocent mentor who was Brainwashed and Crazy. Then Mualim goads Altair to destroy the Apple; Altair says he can't, to which Al Mualim ominously replies before dying "Yes you can, Altaïr. But you won't". He can't destroy the Apple because it now controls HIM!
After Robert throws Altair out of Solomon's Temple, Malik somehow manages to escape with the Apple, despite the fact he's outnumbered, his brother was killed, his only escape is climbing back the tunnel he came in through and his arm was cut open. How did he do it? The Apple did it for him. If the Apple is sentient and can influence others, it can make people act as it wants without them even knowing or realizing it, ever. It's entirely possible it controlled Robert to let Malik escape, but killed Kadar and injured Malik's arm(Or even worse, make Malik CUT HIS OWN ARM OPEN WITHOUT REALIZING IT), just to make it look like Malik escaped all by himself, as well as brainwash both Robert and Al Mualim to make Altair act as Juno wanted him to. The implicationsdon'tstophere. It's not made clear to what extent it can manipulate the human mind, but if it can program minds to act as it wants just from being close to it, then it made Altaïr its pawn for the rest of his days. If it can create illusions and manipulate one's mind and perception of reality, how much of Altair's memories seen by Desmond are real?! Or Ezio's?! Or Edward's, Haytham's or Connor's?!?! For all we know, they could have done horrible things under the Apple's influence that they don't remember! Since there are numerous Pieces of Edens that have come in contact with not just Assassins and Templars, but Kings, Popes, Generals and Prophets (i.e. Cain and Abel, Moses, Jesus, Joah of Ark, Alexander The Great, King Arthur, Attila The Hun, Napoleon Bonaparte, George Washington (and we get to see what the Apple does to him, just think about that), then not just the Assassin vs. Templar war, but ALL OF HUMANITY'S BLOODY HISTORY, has been under Juno's control! You know the Templars you killed that were Asshole Victim?! Well, What if they WEREN'T?! Rodrigo Borgia was Cardinal for years, and the Papal Staff was a Piece of Eden that could have very well made him become the monster he is, the same goes for Cesare! Charles Lee was a great guy, but he suddenly becomes a Politically Incorrect Villain after spending time with Haytham, who held the Grand Temple Key with him for years and Took a Level in Jerkass during the timeskip?! That means that, through all the games, the Assassin has been a brainwashed puppet, killing people who themselves were turned into brainwashed puppets of an abusive precursor. Gone Mad From The Revelation already?!
Tropers often compare the Abstergo Animus to "Baby". Abstergo completely ignores backstory and most of the character development, everything seems completely sterile and stern, just like Abstergo itself. "Baby" has everything the other lacks. Also, the Templars Altaïr kills in the first game all seem to be doing great things in the way they explain themselves and Altaïr seems to have misunderstood everything. Every Templar is like that, with the exception of Majd Addin. His only objective was killing people and gaining more power. Now, if we think this through it could be the Abstergo Animus manipulated Desmond's genetic memory somehow to make the Templars seem like better people than they really were. Except Majd Addin, who did not get that makeover. In other words, even the Templars thought he was an ass.
Why does Maria tell Altaïr about Robert De Sable's true mission and location? It sounds like a Villain Ball at first blush because that is what enables Altaïr to find him and kill him. It's a second trap. Obviously Altaïr would rush there as soon as possible to prevent the Crusader+Saracen alliance and forgo stealth, which attracts more attention to him than normal. Robert De Sable can plant ambushes along the road that Altaïr would have to travel. Even if Altaïr successfully reaches King Richard, Robert can just say, "he's just a lying Assassin" and kill Altaïr then and there.