Anti-Climax Boss: You will have a bunch of weapons that are super effective against the final boss and if you train the right characters to use them, you can kill him fairly quickly.
Also, Valter goes down way too easily and without much ado for someone who's been a major threat for about three quarters of the game.
Each floor of the bonus dungeons has a promoted "boss" monster. In Lagdou Ruins though, most of the enemies will be promoted, and the boss is the only one who doesn't scale — so it's often the weakest enemy on the field by far and has about 2/3 the stats of the surrounding flunkies.
Eirika. Some people think she's fine for being a Na´ve Newcomer and goes through realistic Character Development to become a strong Lady of War by the end, given that her upbringing was solely focused on diplomacy and she made a personal effort to learn swordplay before the game even started. Others think that the game script is sexist for handing her the Distress Ball a few too many times while her brother gets Cutscene Power to the Max. And whether or not handing Lyon the Sacred Stone was stupid, or understandable given their long friendship and the Demon King's silver tongue.
Though generally well-liked, Ephraim is not safe from this either. A cool though impulsive badass leader and the rightful protagonist of the story, or little more than a glorified Canon Sue who seems to be adored by the script as it allows him to succeed at virtually anything while constantly making Eirika hold the Distress Ball.
Whether or not Innes or Seth is a good romantic partner is a point of some contention. Some people find one or both of them sexist, feeling that their protective attitudes border on the possessive, some think it makes sense due to their personalities/upbringings/political positions/etc. and like their supports fine... some fans just get annoyed with all the arguing over her potential romantic partner since that's not even what Eirika is concerned about for most of the game.
Amelia, though unlike most characters it comes entirely down to whether or not it's worth raising her. On the one hand you have those who don't mind Level Grinding in order to get her to catch up with the rest of your army, and thanks to Magikarp Power the results are usually quite good, but on the other hand there's those who think her base stats are just irredeemably awful for her joining time and training her is more trouble than it's worth.
Gheb. While he became an Ensemble Darkhorse meme character (as seen under that trope's entry below), he's notoriously ugly, and some people consider all the rape jokes surrounding him to be in poor taste.
When the Nintendo 3DS rerelease came around, there was some minor consternation over whether The Sacred Stones was really the best GBA representative for the franchise. Most of the people who were complaining wished for Blazing Sword instead.
The Tower of Valni, an optional side area that unlocks in Chapter 10 (and also the Lagdou Ruins, though they don't unlock until the final chapter). Critics claim that it trivializes the game, as the ability to visit it as many times as you like makes gaining experience easy, while defenders point out that, being optional, one doesn't have to use it, so if it's a Game Breaker it's entirely your own fault for visiting it in the first place, and it's a good place for beginners to the series and casual players.
Common Knowledge: No, Eirika and Ephriam do not get married in their Japanese paired ending. The ending is identical to the English version, any accusations of censorship never happened. There's definite Incest Subtext there, but it never goes beyond that.
Contested Sequel: Among the Fire Emblem fandom; detractors say it was too easy and short compared to other games, fans love it for its worldbuilding and the return of various mechanics from Gaiden. Similarly, there is debate as to whether the complex and interesting characterization of the main antagonist makes up for the generally-cliche nature of the plot.
Kyle is a dead ringer for Spike Spiegel, minus the tragic aspects of Spike's backstory.
Gameplay-wise Morva is a slightly weaker version of the Fire Dragon from the end of Blazing Sword and can be beaten with the same tactics.
Eirika's growths and bases are almost dead on with Elibe's Lyndis.
Similarly to Eirika with Lyndis, Neimi's stats are almost identical to those of Rebecca. Unless you make her a Ranger, becoming more similar to Rath or a promoted Sue.
Demonic Spiders: The Baels are actual demonic spiders, but they have obnoxiously high enough physical attack and defense to fall under the spirit of the trope as well.
Double Standard: Eirika is reviled and hated by fans for needing to be rescued twice. Innes needs to be rescued twice as well, and in one of these times it's Eirika who bails him out... but no one picks on him.
Gheb was just some random Gonk that takes little to no difficulty to kill, but the fandom sees him as a Memetic Molester who stabs others to death with his penis.
Lute is also definitely one of the more popular mages among the whole of FE-dom, thanks to her odd habits, her endearing braggadocio, and the related fact that she can back that boasting up with results. (Her married endings being adorable are also a plus.)
L'arachel is one of the most popular characters in all of Sacred Stones, thanks to her hilarious delusions of grandeur, devoted belief in justice, wacky personality, and pretty design.
The S-class weapons deal ridiculous damage to monsters. The game compensates for this by throwing a shitton of monsters at you in the final levels.
Bishops have a class skill that makes them deal triple damage to monsters. The majority of the enemies you face are monsters, so bishops are very powerful indeed. Plus, they're your party's main healers, so their utility does not just extend to monster levels.
Seth, the game's Crutch Character, actually has really good growths, meaning he both starts off and ends up good. In fact, he averages equal to or better stats that the game's non-Crutch Character Paladins. Seth is regarded as so good that a Solo-Character Run with him is considered easier than playing the game normally. The most common Self-Imposed Challenge for this game is simply to ban using him.
The Tower of Valni, a revisitable dungeon that you can retreat from at any time, in short, an infinite source of experience. It's optional, but if you really want to put the screws to the game this is the place to do it.
Hilarious in Hindsight: Ephraim states he would rather be "traveling the land as a mercenary", and Eirika chides him for it. During the game, Erika is pretending to be a mercenary leader.
Ho Yay: There's a fair bit in the game, most prominently in the mixture of admiration and rivalry between Ephraim and Lyon and Eirika's Romantic Two-Girl Friendship with both L'Arachel and Tana.
It's Easy, so It Sucks: As a relatively easy game in an otherwise Nintendo Hard series, it draws this reaction from some fans. Then again, some point out that it's still harder than your average game, so it kind of depends on what context you're using.
At least until the Brutal Bonus Level, which is suddenly able to reduce level-capped characters to fine paste.
Love to Hate: Valter and Riev are just too hilariously and unrepentantly evil.
Moe: Amelia and Myrrh (less in the "super cutesy and adorable moeblob" sense and more in the "sweet child who goes through lots of shit" one).
Moral Event Horizon: Novala from Chapter 6 gleefully traps several Renais citizens in the mountains to be killed by giant spiders during the fight after they fail to work as hostages for Eirika's surrender. When Eirika is horrified by this display of pointless cruelty, Novala just laughs and says that this is war; any atrocity is fair game as long as you win.
Everything Valter does, but special mention goes to his cold-blooded murder of Glen and subsequent lying to Cormag about who killed Glen in order to send him on a misguided Roaring Rampage of Revenge that could possibly get him killed as well. Riev's approval of Valter's savagery puts him over the line too.
Never Live It Down: Much of Eirika's Base-Breaking Character status comes from her being tricked into giving the Sacred Stone of Renais to the Demon King-posessed Lyon, resulting in its destruction.Fire Emblem Awakening DLC even aludes to this by having Old Hubba claim Eirika was "quite naive. Gullible, even".
One-Scene Wonder: Morva makes a badass entrance at the beginning of his chapter and looks like he may be the Eleventh Hour Ranger. Instead, he gets killed and subsequently turned into a dracozombie.
Caellach can be notoriously hard to defeat. He has a close-combat axe... AND a hand-axe. He hits like a damn truck with either one of them, and not even the Lords will survive at Lvl. 20. You have two options: hope that one of your units survive his attacks, or take the easy path by summoning mooks to slowly waste the uses for his hand-axe to THEN bombard him with magic from far away. Also, his in-story rival, Joshua, is a myrmidon/swordmaster, and Caellach comes equipped with a Hoplon Guard, which prevents critical attacks. That being said, there is a simple way to defeat Caellach with Joshua. Bring a thief to steal his Hoplon Guard.
Carlyle on Eirika's route may be even more annoying. He's a Swordmaster, so that automatically means high speed, hit, and avoid. Avoid which is boosted by the throne he's on. Good luck hitting him, and there's no way you're doubling without powerlevelling Joshua or Colm. Both of whom will probably go down in two to three hits. And he has a crit bonus. And a 2-range sword (though he cannot critical at range because of his weapon).
Fighting him is optional, but those trying to finish Eirika's Chapter 13 early are going to have a really hard time with Aias. He's a Great Knight on a Fort (heals every turn, plus a defence bonus) with enough Con not to be weighed down by his weapons, so doubling him is surprisingly hard. And his assortment of weapons is terrifying: in addition to a 1-2 range spear (to threaten Mages trying to bypass his defence), he also has a Silver Blade (one of the strongest swords in the game) and a Swordslayer (an axe that not only reverses the weapon triangle, but deals bonus damage to sword-wielders). His class may make him weak to both armour and cavalry-slaying weapons, but all those but the Armourslayer have unreliable accuracy, made even worse by him being on a fort. And those using Armourslayers will risk getting oneshotted by his Swordslayer. Even though he is also weak to magic, you have to hope that whichever magic users you send against him will be able to either dodge his attacks or be able to tank at least one. The writers seemed well aware of this, since his death quote is praising Renais' tactician for managing to beat him.
And after that, there's Landing at Taizel, which isn't quite as difficult, but still a pain in the ass. Part of the problem with this level is that, while you do get to save beforehand, you don't get to go back to the world map in between. So if you needed to do some Level Grinding? Too bad!
They Wasted a Perfectly Good Character: Morva, the Manakete hero who defeated the Demon King during his first reign of terror, is introduced, killed off, and revived as a zombie slave of the selfsame Demon King within the space of the opening scene of one chapter.
Tier-Induced Scrappy: While loved as a plot character, Knoll is HATED as a playable one for his poor stats and the general weakness of dark magic in this game. Summoners in general are considered the worst overall class, too, though careful use of their summons can prove surprisingly effective.
A majority of the Bonus Characters who have lackluster stats and growths, as well as limited potential.
Visual Effects of Awesome: As with the Elibe games, the battle animations are considered one of the best aspects of the game.
The Woobie: Knoll, to the point that he actually expresses relief in his death quote. Amelia, who is also a Plucky Girl and refuses to let it get her down. Myrrh, who is already a Shrinking Violet.
The country Grado in general has its forces decimated, 85% of its high ranking leaders killed off, the entire royal family killed, and then undergoes a massive earthquake after the epilogue.
What an Idiot: When Fado gave his children bracelets that act as a twin key to Renais' Sacred Stone, he ordered Seth to not tell them what the bracelets were until "the time was right." Seth, who is usually smart, inexplicably refuses to give Eirika a detailed explanation of its true nature — this while her brother is missing, possibly dead or captured, in enemy territory with the second and they themselves are on the run. He only tells her that losing it puts the whole continent at risk from the Demon King after Novala demands it in exchange for hostages and she — not having any idea that it's more than a very important but not magical or world-risking royal artifact — decides that it's not worth people dying over. Admittedly, he didn't know that Grado knew, but after the bracelet had already been stolen once and necessitated a desperate detour, he really should have given her the whole story.
Somehow, Seth also seems to forget that he shouldn't be calling Eirika "Princess" or "Your Highness" in front of other people. In fact, the Easy Mode script (which differs in some areas from the regular script), Neimi actually calls Eirika "Your Highness" later. It's probably how Binks manages to find them so easily in Chapter 9, too.
Duessel, Selena, and Glen's continuing loyalty to Vigarde for what is probably weeks or months after the initial invasion of Renais. Everything we learn about Vigarde in life points to him being kind, fatherly, and gentle. The second that Vigarde opens his mouth in-game, it's very obvious that he isn't anything but at this point. Yet the three generals treat it more like Vigarde had a bad day. Even Glen, who is the first to voice his criticism, still planned on returning to Grado and confronting Vigarde about his actions when Eirika proves that Vigarde lied to him. In Selena's case, Ephraim calls her out on it, since Myrrh tells her everything and yet she still remains loyal to Vigarde.
This has become worse ever since Fire Emblem Awakening has her in the Bride class, despite still being a fighter on top of a staff user. Even more baseless because you can download a version of Eirika that is still a 100% Swordswoman (more exactly a myrmidon, which makes sense since her Lord class is VERY similar to it), so the above "Bride Eirika" is an optional event that can be taken or not.
Woolseyism: Ismaire's original name was Ishmael. Since that's a male name, it got approximated to the more feminine sounding Ismaire.