Anti-Climax Boss: Every one of them, but the most prominient is the Big Bad who comes close to being a Cutscene Boss. The closest you get to having a boss fight with him is when you chase him on a carriage and punch him while falling off a cliff.
Arc Fatigue: Note that this isn't an indictment of the game as a whole; Constantinople is a great setting idea, bomb-crafting is neat, and there are some really good moments...but while Ezio and Altair receive well-received closure, some players and critics felt that Ezio's story was kinda played out by this point, having already completed his Hero's Journey and a post-Hero's Journey.
Awesome Music: The music from the E3 2011 trailer, the triumphant and sorrowful "Iron" (by Woodkid) seems almost written for this purpose. You feel what Ezio must be feeling, from finally reaching his destination, to fighting for his life and experiencing hallucinations, to being dragged to his supposed death. It sums up perfectly the finality and closure the game will bring.
Scheduled for Deletion is very powerful. Considering it's also used in the trailer for The Lost Archive, it may very well double as Sixteen's theme — fitting, especially with that title. A pity it's so short.
Den Defense. Say what you will about the minigame, but the music is amazing.
On The Attack is really badass. Similar to AC 1's post-assassination theme, in that it has a techno-ish feel to it and feels pretty damn intense, except this time, there is an epic distortion guitar and various other instruments at play as well.
UbiSoft is in some kind of competition with Naughty Dog over chase sequences; Sequence 8, Memory 3; End Of The Road has Ezio parasailing behind a runaway carriage, dive-bombing like an attack falcon to dispatch mooks!
The Hagia Sofia level might just be the best Hidden Tomb in the entire Ezio trilogy.
The Minstrel level, which asks you to beat up the annoying bastards, and then lets you pretend to be one, is the Funniest Level Ever!
Demonic Spiders: Janissaries. Ubisoft felt the need to take Papal Guards, the Demonic Spiders from the previous game and make them even stronger. Much more health than a Papal Guard, immunity to execution chains and counter-kills, very strong ranged attacks, and very difficult to hit in melee. Good luck if you ever get into open conflict with one, let alone a group of them. Subverted when you get the Sicilian Rapier, which can kill them all like flies.
Also, Siege Engines in Den Defense, especially the cannon types. They make quick work of your barricades (the cannon types in particular can destroy fully-upgraded barricades in a single hit) and take forever to take down. If there's a single enemy that will end a Den Defense game, this is it.
Game Breaker: Piri Reis sells you bomb equipment with a 15% discount, and will buy it back at the full retail value. Six figures for fifteen minutes work, anyone?
Genius Bonus: There is a hypothesis that suggests that the human population was reduced to around 10k-15k around 70,000 years ago. Look up "Toba Catastrophe Theory". Sure, it wasn't caused by a solar flare, but you know - Alternate History.
It's Short, so It Sucks: Has the shortest main quest out of all the Assassin's Creed games, barring Assassin's Creed Rogue. The sharp reduction in the number of faction side quests as well as the removal of Assassination Contracts doesn't help much.
It's the Same, Now It Sucks: Oliver Bowden's novelization of the game is rather dry, sticking heavily to the source material of the game and adapting the Altair scenes again (Bowden had earlier in 2011 done a novelization of the first game and included what would become Altair's flashback scenes). It's commonly considered the weakest of his novels, largely just for adding nothing the game doesn't give you (Unless once doesn't get Assassin's Creed Embers, which ties up Ezio's story).
The game itself is also criticized gameplay wise for basically being Brotherhood again in a different city, and with the few new additions (tower defense, bomb crafting, hookblade-zipling) hard to get excited for.
Swami, Abbas's Dragon, also deserves some credit for the above actions. He was the one who actually killed Sef and Malik and, when he meets Altair in person, brags about how he told Sef that Altair was the one who ordered him killed. He then kills Altair's wife, Maria as she's trying to stop Altair from killing him.
The Big Bad Prince Ahmet, who took Sofia hostage with her ransom being the Masyaf Keys, but presented himself as a sincere Templar who believed in the ideals of peace through unity (in the same vein as those from the first game) and described their conflict as "two men who should be friends quarreling over the keys to a library." Ezio hands over the keys and Ahmet allows him to go unimpeded to rescue a hooded "Sofia" atop a tower, only for Ezio to find a decoy (although apparently kidnapped to act as an unwitting decoy), then turn around to glimpse the real Sofia being hanged from a tree far, far away.
Well, to be frank, Ezio had already killed most of Ahmet's Templar Agents, including vizier Damat Ali Pasha, who was historically a great supporter of Ahmet for next sultan, and his murder of Tarik Barleti did a great, albeit unintended smear job on Ahmet's reputation. Sultans and princes from Constantinople were known to hold grudges and deal harsh punishments, and in Ahmet's case, Ezio's actions cost him the crown.
"You are getting RICH! Off half truths! And double dealings!" "You are getting RICH! Off half truths! And double dealings!" Repeat until ears bleed.
Nightmare Fuel: Being able to hear the Assassins talk while on Animus Island is pretty creepy. What with them talking like Desmond's not there, and being totally unaware of what he's going through really cements the coma feeling.
It's a little horrifying to make your way up the tower where "Sofia" is being held hostage... only to realize that it's not her, and the real Sofia is being hanged from a tree in a courtyard in the distance.
Also, the Templar stalkers, who can backstab you at anytime. What was Ubisoft thinking?!
Not to mention beating them usually involves graphically jamming their knife into their face. It's up close.
We finally get to see what happens when someone without sufficient First Civilization DNA tries to use an Apple of Eden. It isn't pretty. When Abbas activates the Apple, it goes berserk and starts firing off randomly; knocking Alta´r around and reducing everyone else to writhing on the ground in pain. This includes Abbas himself, who is in the process of being slowly killed by the Apple until Alta´r shuts it off.
In The Lost Archive, finding out that Lucy is a traitor is tough enough. But Ubisoft gets some serious kudos for revealing it just before Clay's breakdown — because you realize that he would have been fine if Lucy hadn't turned on the Assassins, because if she'd remained loyal, she would have gotten him out before the Bleeding Effect could have done any permanent damage. He'd have suffered no breakdown. No insanity. No suicide. She didn't just destroy his life, she destroyed who he was. She stood back and let Vidic break him to the point that killing himself with a ballpoint pen and painting desperate messages on the walls and floor in his own blood was a better option than living. She did that to him. To me, that simple, understated scene carried more weight than any dramatized Reveal.
Also has the distinct honor of retroactively making the player punch of the last game a Moment of Awesome.
Worst of all is probably playing Altair's last moments of life, and knowing it. The game really hits you hard when it tells you to "Sit a moment and rest...", directing you to the very chair that Ezio finds Altair's remains in over 250 years later. Doubles as a Tear Jerker.
So Cool, It's Awesome: Hookblade zipling across Istanbul never gets old. Istanbul as a city qualifies, since its great colours, distinct locations and cornucopia of monuments means that there's always something new to see.
That One Level: The first carriage chase, in Masyaf. Nothing else in the entire game compares to the sheer frustration of a Luck-Based Mission that is required to proceed.
Tough Act to Follow: Brotherhood is seen as one of, if not the outright best, games in the entire franchise. As mentioned in Arc Fatigue above, it's not that Revelations is bad, it's just that it doesn't deliver as well as Brotherhood.