Idiot Ball: Why, in the name of all that is holy, would the most vehemently anti-Shadowlands Clan in Rokugan ever ally themselves with the Shadowlands during the Clan War? Ask Hida Kisada, who apparently thought it was a good idea, and paid for it dearly... like pretty much anyone else in the Clan should have been able to tell him.
Characterization Marches On: It made slightly more sense before the setting was entirely fleshed out, before the Shadowlands was revealed to be a literal geographic location as well as the ultimate evil in the setting, and before it was established that the Crab Clan's duty to guard against it. Until the game's first expansion, it was really the Crab Clan itself that had been the bad guys.
Designated Villain: This is the Scorpion Clan's job. The first Emperor Hantei asked the Scorpion to be the bad guys that the other clans can fight against in order to insure that the clans never unite against the Empire.
Magnificent Bastard: The Scorpion Clan specializes in this trope, but there are plenty to be found among the other clans, as well.
Including at least one Scorpion-trained Emperor (Toturi III), and current Emerald Champion, Shosuro Jimen.
Evil Is Sexy: Even though the Shadowlands Taint can either make you horrifically ugly or inhumanly beautiful, most Tainted women have tended to remain on the "inhumanly beautiful" side of the spectrum. Hmm...
Well it goes without saying that the supporters for each of the factions (even ones no longer active in the game) are pretty passionate and will defend their faction with great zeal. One can even find intense debates and divides within a single clan (the Shinjo vs. Moto flame wars among the Unicorn player base have been going strong for over a decade) to say nothing over the debates about which CCG ruleset was best, First Edition vs. Third Edition RPG, CCG vs RPG (judging just from this page), etc. etc. etc...
RPG versus CCG gets special mention, because the Metaplot is the chief draw of the CCG: the ability to affect the story of Rokugan through tournament victories and behavior. However, the current consensus among RPG players in general is that metaplot is absolutely toxic to a game line and hinders GMs' ability to tell their own stories. In addition, many of the RPG players consider the Story Team's endless rearrangement of Rokugan to provide new cards to buy and new tournament prizes to be detrimental to the lore, if not outright Canon Defilement. The writers for the Fourth Edition of the RPG are very Genre Savvy about this, and do their best to make sure that there are rules for playing in any era that the GM wants to run a story in, avoiding being drawn into the metaplot.
By and large FFG's procurement was met with celebration of the fanbase, but discussions of what FFG could - or even should - change or take out of the game have led to many, many heated arguments from all corners of the playerbase.
Complete Monster: Hantei XVI, known as Otomo Okucheo before his ascension and also known as the Steel Chrysanthemum , is the most violent and tyrannical Emperor that Rokugan ever had. He was ambitious even as a young child, when he arranged for the murder of his brother to prevent him from being made Emperor. His atrocities ranged from the disastrously grand, such as creating a Secret Police force to hunt down traitors and political dissidents; to the disturbingly petty, such as torturing a woman to death for protesting his widespread use of torture, and then naming her as a minor goddess of Torture. He ruined a political opponent's reputation and career, just so he could claim the man's daughter as a concubine. When that daughter refused to bear Hantei XVI a child, he had her imprisoned in her own room and forced the matter. The final straw, however, was ordering the execution of his own mother, because she dared to protest him killing all of his siblings so they couldn't contest his claim to the throne. This final act was enough to make his entire guard, horrified by what he had done, turn on him, assassinating him in spite of the fact that they would all need to commit seppuku afterwards. Back from the Dead more than 500 years later, Hantei engineered the 12-year-long War of Spirits in order to try taking back the throne. After the War, as one of the conditions of the treaty, Hantei tutors the son of an opponent. Planning to attack his student in order to cause the treaty to be broken and war to break out again, Hantei, while beating this student, is killed by his own fiancé, who has grown to care for this student.
When Hida O-Ushi's uncle Tsume scornfully asked her (formerly Unicorn) husband Hida Yasamura whether he would have the resolve to cut O-Ushi down if she was slain and raised as a zombie. Yasamura replied that it would be impossible for him- because if O-Ushi was slain, he would already be dead.
Of all people, Hida Kisada had two: one, when realizing his son Hida Sukune, whom he had sacrificed to Fu Leng, had returned as a sacred spirit AND forgiven Kisada. Later, after Kisada's own resurrection, he found a previously unknown heir, a Dragon with less concern with battle than with law, and showed the boy favor anyway — proving that even Kisada can change.
The Interspecies Romance between Daini and Mara is a subtle one, but it's really quite sweet — and very significant, when one remembers that these two had to overcome serious obstacles, including very alien appearances in each other's eyes, completely different racial psychologies, and his own culture's traditions of arranged marriages, stoicism and opposing of romantic love. Yet, despite it all, they managed to fall in genuine love and marry because of that love. "Legacy of the Naga" even has a throwaway line about how Daini is perfectly comfortable allowing Mara to assume her true, tail-slithering form as opposed to needing her to be in her bipedal form, and even enjoys her coiling embrace.
Shoju Bayushi's wife, Kachiko, once asked, revealed to him that she'd been having an affair with Hoturi Doji, and that Shoju wasn't their son's father. After a tense moment, the boy was brought in, with Kachiko expecting Shoju to kill him. Instead, the maimed Scorpion picked the child up, declared him his heir, and said that, as the child of the woman he loved, he would care for the boy like his own.
The legendary Kaiu engineers of the Crab Clan spend most of their time building and maintaining the armor, weapons and siege engines that the Crab rely on for survival, and that's when they're not working on the Great Kaiu Wall that separates Rokugan from the Shadowlands. When they have spare time or need a break from the ceaseless grind of war, however, they make toys for children. People may not like the Crab Clan, but no one turns down a gift of a Kaiu toy.
Dork Age: What many people consider The Hidden Emperor Arc to be.
Some people throw Diamond and Lotus Editions onto that pile.
It's pretty uncommon to find someone who liked the Destroyer War, as the Spider were the only clan that came off as even slightly competent. Subsequent developments (the Spider becoming a legitimate Great Clan, Fu Leng taking over Jigoku and joining forces with Daigotsu to save the Empire, taint only affecting the willing) have been similarly poorly-received.
And the third edition of the RPG had pretty terrible proof reading, including an appendix in Emerald Empire with NPCs with Honor stats sometimes twice as high as the rules allowed and a revision of a rather important rule in the Revised core rulebook that made the Defense skill unintelligable.
The Ivory Edition era is so poorly received that AEG's staff are begging people to stay.
Fanon Discontinuity: As far as many older players are concerned (especially those who play the RPG), the canon storyline ended with the Second Day of Thunder and Toturi I becoming Emperor.
The Destroyer War, Daigotsu taking over Jigoku and making the taint voluntary, and forcing Iweko to make Spider a Great Clan is being treated as discontinuity as well.
Idiot Plot: The sheer amount of stupidity required to allow Hantei XVI to come to power, and then continue to reign after it was clear that he was insane, is mind-boggling. Hell, his birth was presaged by horrible omens and portents unseen since Iuchiban, and all the major families just chose to ignore it!
The Spider's ascension to Great Clan status involved the Empress agreeing to a bargain with Daigotsu, immediately after Daigotsu broke their previous one, and all clans but the Lion just shrugging and accepting it — including four clans who'd attempted to overthrow Emperors who'd done less than openly bargain with the Shadowlands.
Memetic Badass: Yoritomo of the Mantis and Moto Chagatai of the Unicorn have reached Chuck Norris-level badassery in some circles.
Promoted Fanboy: Almost everybody currently in charge of designing the game or writing its material started out as a player of the CCG or RPG (or both).
In story, Toku went from being a peasant, to being a friend in the retinue of a disgraced ronin leader, to being a favored ally after said ronin leader became Emperor, to leading a minor clan. After his death, he was promoted even further to become the Fortune of Virtue. His daughter married into the Scorpion Clan, where she is now leader. Some players consider that if the Scorpion had selected her as a candidate for Emperor, they may have won the Race for the Throne by consciously invoking this trope.
Screwed By The International Olympic Committee: During the game's tenure at Wizards, the IOC sent legal notice to Wizards that the logo for the game (five interlocking gold rings in a pentagon shape) was a violation of the IOC's treaty-protected copyright of their logo (five interlocking rings of different colors in a "W" shape) on the grounds that the treaty claims any design with five interlocking rings, regardless of orientation or color. Wizards changed the card backs (which prominently featured the logo) to a new design that instead incorporated five independent gold discs. This had the unintended effect of essentially banning any cards produced before the change (for the simple fact that they'd be easy to spot in a hand) unless the player invested in opaque-backed card sleeves.
Tear Jerker: Hoturi dying in Kachiko's arms after defeating Fu Leng in the Second Day of Thunder. While she forgives him for killing her son (and though he did not know at the time his son too) during the Scorpion clan Coup and they reaffirm their love for each other.
And then later, to permanently bind Shosuro to the lake beneath Kyuden Bayushi, Kachiko drowns herself in its waters knowing full well that her soul is likely to be bound and she won't be able to move on to the Heavens. Her last sight before going under is Hoturi, newly resurrected, reaching the side of the lake.
Kachiko inspires many of these. During the coup, Hoturi proudly kills Bayushi Dairu, the heir to the Scorpion leadership. It isn't until years later, as Hoturi's pondering Kachiko's sudden and passionate hatred for him after years of saying little to one another, that Hoturi realized the truth: Dairu wasn't Shoju's son, but Hoturi's.
That One Disadvantage: Momoku. You can't spend Void Points. Imagine if you couldn't spend Willpower in The World of Darkness and you have an idea of how utterly this will screw you. Worth ten Character Points (the most of any disadvantage); not even remotely a fair deal.
It's now only worth 8 points, and only prevents you from using the common Void Point expenditures. You can still use Void Points to activate Techniques that require them.
Dark Fate. When the GM feels like it, you will betray everything your character holds dear, most likely including the other players, and probably become an NPC, if not dead (or a Fate Worse Than Death).