Anti-Climax Boss: If you prioritise story progression over character development, then the final boss fight can be Very Hard. If you end up with a high-level party because you've been on a long Fragment hunt or something ... not so much.
Bad Export for You: The PC version will only have the Japanese voice acting in Asia. While a minor issue, it does get on some fan's nerves. At the least the price for the game is cheaper in those regions.
The main antagonist Caius is either a well-written, sympathetic, yet still totally badass Anti-Villain, or an absurdly overpowered villain who is difficult to take seriously. There is also a remarkably deep divide over whether he's cooler and more powerful than Sephiroth.
Big-Lipped Alligator Moment: During the introduction of the game, Serah spontaneously has her clothes change from her XIII outfit to her clothing in this game. While she and a couple other characters comment on how strange it is, none of them dwell on it beyond a brief mention, and no explanation or reason for why it happened is ever given.
Academia 4XX AF. This comes after the long Augusta Tower segments, and before Episode 5. There are no enemies, and your visit may be very quick, depending on if you collected the Graviton Cores.
New Bodhum 700 AF. You arrive right before the final dungeon, but the enemies are easy and, minus cutscenes, your visit will be over in minutes.
As an optional area, Sunleth Waterscape 400 AF. All seven Fragments are easy to collect, and the boss battle is a joke (of the easy and funny kind).
Oerba 300 AF and 400 AF, where a small number of base fights are interspersed with paradox events, where you not only get fragments, but gain a side story about Mog in the process.
Broken Base: The ending of the game is quite a Downer Ending, and also rather confusing, causing the fandom to split between hating the game for its ending or defending it for other merits and saying those who think it's bad "don't get it".
Saboteurs: Black Chocobo, Celicerata, Jihl Nabaat (DLC)
Synergists: Yakshini, Sazh (DLC), Purple Chocobo
Medics: Flanitor, Green Chocobo, PuPu (DLC)
Contested Sequel: With so many changes from the original XIII, both in gameplay and story, this was inevitably going to happen. The general rule of thumb is that people who disliked the original found the sequel to be an improvement in most respects, while those who enjoyed the original judged this one to be an exercise in dumping babies with bathwater. This trend would continue into its own sequel.
Die for Our Ship: Alyssa initially suffered this just because she was shown being close to Hope in the previews. Then the fans actually played the game, and discovered she was The Mole and tried to kill Serah and Noel. It didn't help.
Disappointing Last Level: Academia 500 AF is a long platformer section with rotating platforms, switch puzzles, and enemies that are a jump in difficulty from the previous areas. It's often criticized for slowing the game to a crawl right before the final boss.
The Arbiter of Time makes only one sinister appearance in the base game, and the Coliseum DLC doesn't expand much on him despite being its host and a Bonus Boss. This hasn't stopped fans from hailing him as an incredibly cool character who would wreck Caius if not for story purposes; they're similarly disappointed by his absence in the following game.
In a more meta sense, the game itself, thanks to taking it's predecessor's gameplay and refining it while adding more layers of depth to an already deep gameplay system.
It was pretty large in XIII, but now that Hope has aged-up, oh, ten years, expect Hoprai shippers to be royally pissed if Lightning and he don't get together now that the can avoid otherwisesquicky implications. Hilariously, by the time they actually get together in the next game, Hope is 14 again.
Noel and Serah shippers seem to be popping up everywhere as well, mostly due to the fact Snow left Serah in New Bodhum to look for Lightning and they work pretty well together during their travels.
Dragoons are a pretty good early example: capturing them is pretty easy, they don't take much materials to level up and their Strength is generally double or triple that of Noel or Serah in that point of the game.
Getting Lightning's DLC episode as early as possible (and spoiling most of the ending in the progress if you don't skip the cutscenes) allows you get her as a monster ally at any point in the game if you 5-star both of her battles, which is pretty easy to do as the levels in her episode are independent from the main story and thus 5-starring her battles is just as easy or hard at the end of the game as it is at the very beginning. Pretty much all the DLC contents count as this, the Coliseum DLC alone allows you to get the best Ravager (Lightning), best Sentinel (Snow) and the best Saboteur (Jihl) monsters in the game, although in their case you at least need to be strong enough to beat them first.
The Sazh DLC. At the start, you are given 10,000 Casino coins and are told to go play. Bet them all on one of the card games, win and you might end up with around 50,000 coins. The kicker? These original 10,000 coins are free and Serah and Noel get to keep everything you win as Sazh, enabling you to buy out the entire casino as soon as you set foot there.
While you can avoid enemies, some are just relentless. Some are as fast or faster than you. Others have a seemingly endless 'sighted you' zone. Why is this annoying? Well, from how the game's mechanics work, it means you have no other choice but to fight, whether you want to or not.
The Cie'th of Academia 400 AF, mainly because they won't go away and have a wide aggro range, leading to instances where you have no clue what you just ran into.
While some DLC are well-received, a part of the fanbase doesn't like how Square is implementing it by making some of it available and advertised on day one. Square has stated that this is the first title they're working on to have planned DLC in one of their titles from the start of development, which doesn't help their cause.
The scenario, especially the ending, led to a lot of bashing from the fanbase.
Iron Woobie: Lightning could be seen as this. She was erased from history save for the memories of a select few people, pulled into a chaotic, dead-looking world with no people and doomed to do eternal battle with her rival to protect Etro. And she ends up being Taken for Granite during the normal ending.
Jerkass Woobie: Alyssa, who is motivated by a legitimate fear of being erased from existence.
Most Annoying Sound: The slot machine makes a loud 'BA-DUNK' sound every time you get two Microchus in a row. Three Microchus is the ultimate jackpot, but you'll virtually never win it outside of Super Victory Mode. The game knows this, and loves to tease you with Microchus.
Offscreen Moment of Awesome: Much like it's prequel, this game contains backstory for events and characters in wikipedia-esque entries in the datalog and fragments. For instance, some fragments shed light on Caius' past. It would have been awesome to see him duking it out with his predecessor or performing the Incarnate Summoning of Bahamut.
Academia 400 AF, due to the high encounter rate and the fact that you can't run from any of them. At least it's a great place to grind for CP and Gil if you need either.
Academia 500 AF. An unexpected platforming segment with long waits for platforms to get in correct positions (and featuring a few extremely difficult enemy encounters), the area was often criticized in reviews for slowing the game down to a crawl right before the big finale. Mapping the area to 100% is an even bigger chore.
Academia 4XX AF just because of the Captain Cryptic quiz. He'll randomly spawn in any area and the only clues you'll have are from the townspeople which isn't really helping that much.
A Dying World 700 AF, mainly because it's a bitch to get from one point to another, and there are tons of hidden treasure chests.
If you dislike the time distortion mini games, then you will HATE Oerba 300 and 400 AF. Running around the same small map playing the three distortion mini games *over and over*. Some of them have 6 stages, and there are 8 or 9 per time period.
Scrappy Mechanic: The Hands of Time in the Time Warp Anomaly sections. Do you suck at math? Yes? Do we have a minigame for you. Some of them that have a time limit. Oh and some of them also are randomized as well. "Oh, but surely there's a guide"- Guide my ass! Every puzzle is totally freaking random!! Mitigated now that people have made multiplepuzzle-solvers for it. Of course, that doesn't improve the mechanic itself; just make it less annoying.
Ship-to-Ship Combat: Snow/Serah shippers and Serah/Noel shippers go pretty hard at one another.
Surprisingly Improved Sequel: The general consensus is that this game is much better that XIII and Lightning Returns. So much so that Famitsu gave it a perfect score.
Tear Jerker: The true ending, if you ignore the Soundtrack Dissonance, is this is a nutshell. Serah dies, Etro is dead and the entire world will die with her, Lightning is crystallized (by her own choice, as stated on a Fragment), and Caius has won.
The first battle against Caius, for those who haven't touched the sidequests yet. He can heal himself and buff himself up.
The Paradox Scope battles with Caius at A Dying World 700AF and the Void Beyond, with Serah (and Mons) and Noel going it alone respectively. If you're properly leveled with above average monsters in your corner in Serah's case he shouldn't be too much trouble, but he's not to be underestimated because he can still do alot of damage in short time. Weaker characters may be forced to use Wound, which reduces max hp (useful because once you kill him he instantly revives).
That One Sidequest: The goddamn Lucky Coin fragment. To get it you have to win 7,777 coins at the slot machines. And no one seems to be able to agree on whether that's a total number across all plays or all in one sitting (luckily losses aren't counted against that number), but either way expect to lose A LOT of coins, and thus gil in the process.
They Wasted a Perfectly Good Character: Alyssa. Think about it, had they somehow decided to throw her in as one of the three main party members, her dilemma would be much more profound and so many layers could have been added.
The Prada advertisements are getting in on it, despite the game being nowhere near it. Sazh's outfit, however, is getting universal praise. Lightning is generally well liked. It's Noel in particular that everybody doesn't like.
There is a cutscene near the end of the game with Noel, Serah, Hope and Mog on an airship. It has a more detailed render than the other cutscenes, and while every individual part of their faces is more detailed, the general effect is a little bit off.
When the trailer was first released, along with the logo picture, there was more than one person who commented on Lightning's "sexy female rival."
Many seem to be confused about Mog's gender (which is canonically male).
Viewers Are Goldfish: Possibly in response to criticism of the first game, this one has a bad habit of heaping exposition or repeating things mere minutes after they've been brought up. Unfortunately, it's not usually done subtly, instead hitting you over the head multiple times until skipping scenes suddenly doesn't seem like such a bad idea.
Violation of Common Sense: In Chapter 4, a shadow clone of Lightning asks Serah to come live with her in the (obviously fake) dream-world they're in. Saying no will advance the story. Saying yes will give you an alternate ending, a whole bunch of experience and place you right back before the question.
Yeul, or rather the many reincarnations of her. No matter which Yeul it is, she's born with the Eyes of Etro which lets her see the future and everytime she uses her powers (Which is often against her will), it slowly chips away her lifespan and she dies young.
Serah, due to having the Eyes of Etro as well. And the journey she takes ends with her death.
Noel as well. He's from a time after the end of the human race and is the last human and his only goal is to save humanity from extinction, even if it erases him from time.