Anti-Climax Boss: Rodrigo Borgia. The fight has an interesting bit of both him and Ezio using a Piece of Eden, but the idea isn't taken advantage of and afterwards it just descends into mashing the melee button on him.
Those beggar women who constantly got in your way in AC? They're back in the form of wandering minstrels. Except this time, so long as you don't pull out your weapon, the guards don't mind if you start a fist fight.
Or you can finally throw gold at them to distract them. They're like pigeons.
Practically every complaint with the original game was addressed in Assassin's Creed II. Too repetitive, not enough mission variety? Every assassination has a much more varied sequence of events leading up to it, instead of "gather information, stab mark in face." Uninteresting protagonist? Ezio is a lot more relatable than Altaïr. No tangible reward for collection sidequests? Now there are, and a full-blown inventory/resource management system to boot. Can't shake the beggars off? Ezio can toss money on the ground. Framing Story doesn't make sense? It still doesn't make much sense, but it's been expanded upon in a manner that shows that there are interesting answers to the many (many, many) questions brought up by the first game (as well as loads more Genius Bonuses for history buffs). Long cutscenes to establish evilness of victims? Save it for narration instead. Trippy, five-minute-long dialogues with dying victims? Shortened to less than a minute.
Mercenaries are very good at distracting guards, but the game-breaking comes from the fact that attacking any enemy who is engaged with an opponent from behind is an instant kill if you're close enough. You can wipe out dozens of guards without breaking a sweat using mercenaries like this.
Smoke bombs, to a lesser degree. Pop one, and every guard in a surprisingly large area is helpless for about ten seconds, plenty of time to One-Hit Kill most or all of them.
Mercenarii and smoke bombs are the two main ways to get the "No-hitter" achievement (kill 10 enemies in a row without being hit while remaining in combat), albeit with mercenarii you have to hit at least one guard first to initiate combat.
If you're in a fight with guards you can't win or don't want to put the effort into winning, you can lob throwing knives at them. They're unblockable and only one (Florence/Tuscany/San Gimignano) or two (Romagna/Forli/Venice/Vatican) are needed to kill any guard in the game. If you feel the need to use them up-close, you can also pay a one-time fee for "special weapons" training to throw three at once, though the "charge up" animation before the actual throw can be interrupted.
Hidden Blades are this if your timing is consistently good enough; while its "window of opportunity" is smallest out of all weapons (unarmed is equal or a close second), they are the only weapon to always have a fatal CounterKill against any opponent not named Francesco de' Pazzi (at il Duomo) or Rodrigo Borgia/Alexander VI, irrespective of the opponent's Health. Other weapons only have CounterKills if the opponent's Health is low enough or if they're suddenly vulnerable (disoriented by smoke or sand, distracted by a NPC, just got disarmed, knocked down, bumped into, and so on).
Agiles, though they don't do well in a stand-up fight, can run you down if you try to flee, even when you're sprinting all-out. If you must run, your life will be made slightly better by at least slaying them first.
Growing the Beard: Figuratively and literally; it marks a major increase in the substance of the storyline of the series and saw the potential in the first game's gameplay and design lived up to fully, as well as Ezio growing a Badass Beard in the Time Skip of recovering from a major stab wound between the DLC sequences.
For a very long time, the page quote for Munchkin on This Very Wiki was: "Munchkin: One who, on being told that this is a game about politics and intrigue in 17th century Italy, asks to play a ninja." The latter part of that sentence has since been potholed into the main page.
Subject 16's hysterical ramblings include a past life where he seduces a woman at the opera and talks about having sex with her. This becomes rather amusing when you know that his voice actor Cam Clarke is openly gay.
Ask half of the fanbase what they think of Leonardo and Ezio.
During the mission where you rescue Bartelomeo, he calls you "Madonna" and "bella mia" (my lady).
Iron Woobie: At the end of the game, you'll find Ezio to be one of these if you think about it a little. Ezio started as a young nobleman who was really just out to live life. His interactions with his family members showed that he had a loving relationship with each of them. Suddenly, his father and brothers are executed in front of his eyes forcing him to run and start a life of ceaseless bloodshed. Then when he finally defeats Rodrigo and has the opportunity to take revenge, he stops and says: "No. Killing you won't bring my family back." He proceeds into the Vault and Minerva essentially tells Ezio: "Your job is done, now shut up." And as of Brotherhood, his troubles seem to be far from over. Poor Ezio...
Jerkass Woobie: Many of Altaïr's and Ezio's victims turn out to be simply misguided but well-intentioned people with their final words.
The comments on Stephen Plays video on the time-skip are full of "Get stabbed, grow a beard.".
Porting Disaster: The PC version, at launch. Runs like molasses going up-hill in January (with crutches!), about as stable as nitroglycerin and has a DRM system so draconian that it makes all predecessors look good. These issues have been fixed, to an extent.
Scrappy Mechanic: A small but very annoying quirk of trying to blend into moving crowds is that Ezio moves at a different speed from the NPCs; depending on how far forward you push the analog stick, he either moves faster than them or slower than them, forcing you to alternate your speed to stay on pace with them. Thankfully in Brotherhood, this was fixed so Ezio automatically matches their speed.
Shocking Swerve: Rodrigo Borgia becoming the Pope for anybody that wasn't aware of that happening in Real Life since prior to that the game never tells the player much about who he is besides him being the leader of the Templars.
Carlotta Moro's letter to the mentally-crippled Dante Moro, where she hopes that someday her former husband will be able to remember her and that she believes he still loves her, even with his mind destroyed. You only get to read this letter after: you've killed Dante.
The title sequence is this for anyone who knows what happens to Ezio's family only a few days after that scene. The music that plays during this sequence seems designed to bring tears to the eyes.
"Port Authority", the Merchant assassination mission in the Bonfire of the Vanities DLC is much harder than it would seem at first glance You have to kill a guy who's tucked into a very secure spot on a small galleon, while 10 guards with super senses patrol the deck and the surrounding pier. Oh, and did we mention you have to kill him without being detected? This mission alone will make you regret ever getting the DLC. Especially considering the rest of the missions before (and after) it are exceedingly easy.
If this happens, you're doing it wrong. Shooting the shmuck that's walking on the docks will get most of the guards off the boat, letting you swim around to the other side, yank one of the guards off the boat via a ledge assassinate, double-spike two guards from behind, and then jump directly down onto the target. It requires good timing, but it's doable once you figure it out.
The assassination mission "Town Crier." Sure, it's a pretty fun mission, but more than likely you'll end up getting shot down by an arrow from an archer you forgot to kill. Even if you do kill all the archers before you reach the tallest tower, by the time you get there, you may jinx yourself into falling hundreds of feet to your death, at which point you have to start the whole level over.
Tough Act to Follow: Is still the most critically acclaimed and beloved entry into the Franchise namely for having a sprawling story and large cast of Historical-Domain Character, jaw-dropping period architecture of monuments, a charismatic hero and for making the most improvements on the formula.
Lucrezia Borgia. After her son's physical recovery the boy was recovered and raised in the Borgia household, but with Cesare posing as the father and Lucrezia forced to pose as the aunt (coincidentally, zia in Italian).
Giovanni Borgia, as lampshaded in Project Legacy.
Erudito: What did the Shroud do to this poor kid? He should be dreaming about the Renaissance equivalent of sunshine and lollipops, not murder and politics! I've never seen anything like this!