These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Raijuta: He's a big, muscular man who appears to be a genuine threat when he first appears, but as the story progresses he's eventually shown up for the weakling he really is compared to Kenshin. This is even more obvious in the manga; in the anime, he at least had an imposing force of samurai warriors to back him up.
Usui: Gets a huge build up, but is defeated by Saito in the space of less than ten minutes screen time.
Yatsume: Again, he's a victim of the "Saito effect".
The Su Shen: Even admitted by the author: they're only there to keep Saito, Aoshi, Sano and Yahiko occupied.
Anvilicious: Considering Kenshin's non-killing vow, the series does have shades of this, with Kenshin often saving his enemies in almost any circumstance despite the often intense enmity to him.
Badass Decay: Raijuta was supposed to be a bigger threat until Watsuki remembered that Kenshin had already demonstrated the ability to dodge bullets.
Kenshin has a little of this in the Kyoto arc but this was due to Watsuki's Character Development of Kenshin as he didn't want him to be an Invincible Hero and brought him strong enemies.
However, because it was such a new thing at the time, Watsuki kept getting in trouble with his editors, who demanded he make the series more male-targeted (observing the strict gender segregation shonen manga had at the time). Several times in early volumes, Watsuki apologizes for the series being more popular with girls than boys.
Broken Base: The manga versus the anime versus the OVAs. Fans of each rarely overlap (although the anime and OVAs have some overlap, for obvious reasons).
The fans who dislike the OVA's are extremely vocal about it. Read any RuroKen entry on this site (or any site discussing anime) and you're bound to find some snide remark about it. Unfortunately, that wrath is also typically visited upon any fans who don't hate the OVA's.
Ditto Season 3 of the TV series. The most vocal RK fans write off that season entirely, considering the series to have ended at episode 62. They get quite offended if anyone suggests there were any decent episodes in there.
An anime reviewer who had heard the complaints about Season 3 decided to actually watch it objectively, concluding that the Christian arc isn't that bad (though it is long and nowhere near as good as the Kyoto arc), and the filler is actually decent up to episode 82. It's those last 12 TV episodes where things completely derailed. The video-only episode 95 is considered good even by fans who hate the rest of the season.
There are heated arguments in Japan over the final battle of Kenshin and Shishio in Shin Kyoto Hen Part 2 regarding its controversial ending. Shishio's skull starts to crack from the pressure building up in his body as it overheats, but it's held together by his hachigane. Kenshin kills Shishio by aiming a blow from the butt of his sword at the hachigane, shattering it and allowing his head to split open. Yes, Kenshin actually killing Shishio despite his vow affected the fanbase. To make it more surprising, he isn't even shocked about murdering him.
Gein, Enishi's Dragon. He's a Psycho for Hire, Blood Knight, and an all around sicko who joins Enishi's campaign and offers him advice on Mind Rape-ing Kenshin, not for revenge, but for kicks and a chance to test his abilities. He makes puppets out of corpses, kills everyone who crosses his path, works as an arms dealer, sees war as a chance for fun and intellectual masturbation, and was the mastermind behind the plan to fake Kaoru's murder, just to screw with Kenshin's head.
Most of the major antagonists are sympathetic (and quite Bishōnen to boot) and rank consistently in the top ten during character polls. Watsuki later attempted to avert this by making the antagonists of the Jinchuu Arc Complete Monsters. It didn't necessarily work.
A specific example: Enishi's back story is tragic, but that doesn't excuse his illegal activities and outright sadism.
Best example is probably Soujirou, a minor villain in the Kyoto-arc who stole every appearance he made. Word Of God is that he intended to bring Soujirou back at some point because he felt underused for all the fans he had, but he never did.
Also Okita Souji, who ranked decently in the first character popularity poll (something like 7th place?) despite having only appeared in two or three panels in a flashback at that point. Interestingly, Watsuki based Soujirou on Okita Souji (they're practically twins), and notes in Soujirou's profile that Okita has always been incredibly popular among Shinsengumi fans. He credits this for Okita coming in so high on the poll.
Every one of Kenshin's rivals has this to some degree.
Sanosuke X Saito might as well be canon... (it doesn't help that Sano acts verytsun towards Saito, and his reaction to seeing Saito alive again after Saito had disappeared in the collapsing enemy lair...)
Kenshin to Sano, most obviously in the anime: the adaptation adds one last duel between them not present in the manga, and when Sano collapses from pain, Kenshin catches him and lets out a rather tender smile.
One of the prototype one-shots had Kenshin see this between Megumi and Kaoru (he says something to the effect of "Oooh, so that's why she doesn't want to get married."). They were sisters in that universe.
Enishi. Yeah, he did go through lots of heartbreak, but he also made others completely broken.
For some fans, Sadoshima Houji becomes this after he kills himself. Also an in-story example, as Kenshin expresses pity for him once he's told about that.
Amakusa's Start of Darkness comes when he's a child and both his parents and his whole Christian village is slaughtered, with only him and little Sayo as survivors. Doesn't necessarily mean he was less of a bastard as an adult.
Kenji in Seisouhen had a horrible childhood with a constantly absent father and a mother dying of a grief and skin disease she caught from said father, but it doesn't make him any less of a brat, when he refuses to come back and let both of his parents say goodbye to him before they die, and runs away to Hiko to find "real strength".
Love to Hate: Shishio Makoto is a brutal Social Darwinist who causes many atrocities in the series, yet his odd sense of honor makes him the perfect adversary to Kenshin due to his genuine desire to make Japan strong. The author Watsuki even considers him his favorite villain of the series.
Magnum Opus: As a defining work in Jidai Geki and Shonen manga, it's considered Watsuki's best work and probably the reason why his later manga get overshadowed.
Non-Japanese Love Samurai X: The Sony/Animax dub is surprisingly popular overseas. This is in spite of a few name changes to the primary cast (Kaoru->Kaori and Yahiko -> Yoshi); the dub in question does start to grow a small beard around the time the Shishio arc kicks off, though, with a particularly solid performance from Shishio himself.
The series got immensely popular all over the world. Some famous examples are Latin America, a big chunk of Europe (specially France, Spain, Italy and, to a lesser degree, Germany) and Eastern Asia. In all of those places, the series is considered an all-time classic, and it still has reruns and re-prints.
One of the most iconic cases is Spain. The series arrived there in the summer of 1998 under the name "The Samurai Warrior" ("El guerrero samurai" in Spanish) and became the most watched program of the station it was in. It became an instant classic for Spaniard anime geeks, which is specially surprising when you consider the station treated it as a Saturday morning cartoon. The manga came one year later and rights were acquired by the Spanish branch of Glénat, a French publisher. That branch was at the brink of bankruptcy when they started to publish it, but the success of the manga was so big that practically single-handedly made Glénat the biggest manga publisher in Spain. Thanks to that success, Glénat could acquire other big hits like Love Hina, Naruto, Bleach, One Piece, and many more... Wow! Spaniards Love The Samurai Warrior indeed!
Americans Hate Tingle: Emphatically does not apply to the show – RuroKen hit pretty big in America – but rather the above-mentioned dub. Due to various issues, North America originally got its own English dub commissioned by Media Blasters (this is the one aired on Toonami and available on DVD). This dub is much more faithful to the Japanese and has no name changes. It's also widely considered to be much better acted. American fans who are aware of both dubs' existence universally hate the Animax dub. Amusingly, Richard Cansino plays Kenshin in both dubs.
Hatarakitakunai degozaru! Zettai ni hatarakitakunai degozaru!!" (働きたくないでござる！絶対に働きたくないでござる！！; I will not work, there is no way I will work!) A Japanese meme that heavily implies Kenshin's status as a NEET.
Seasonal Rot: Anime only. Everything after the Kyoto Arc was filler and widely agreed to be inferior to the rest of the series.
Fans who argue the above forget that over a third of Season 1 was also filler, and the Raijuta arc was changed so much as to be completely unrecognizable (the only things that arc has in common between media are Raijuta's technique and Yutaro's fate).
Four episodes in Season 3 are actually taken from an officially-produced novella ("Voyage to the Moon World"; the novel's author is given story credit). Not technically canon, but not made-out-of-whole-cloth filler either.
Watsuki might disagree about it being confined to the anime. He was unhappy with the way parts of the Jinchu arc turned out, particularly the battles against The Six and many of their character designs (one was a pretty blatant rip-off of Venom). He also admitted the... thing... with Kaoru was badly executed.
Strawman Has a Point: When first confronting Kenshin, Saito suggests that his refusal to kill his sworn enemies could indirectly endanger the innocent people he cares about, and in fact already has multiple times. This is supposed to be Saito's Hannibal Lecture, but many fans think he not only makes a damn good point, but exposes the critical flaw in Kenshin's philosophy. Several times throughout the series before and after this point, Kenshin's friends are at the mercy of enemies he formerly refused to kill, and survive by getting lucky.
Viewer Gender Confusion: Kenshin. Not helped by being voiced by women in that Japanese version: ex-Takarazuka actress Mayo Suzukaze in the anime, Megumi Ogata in the CD dramas. There's also a story that he inspired the character Baiken in Guilty Gear when the character designer for the game mistook Kenshin for a woman.
In volume six of the manga, it is revealed that she is one of the top six dojo masters in Japan and has earned the nickname Kenjutsu Princess – many boys at the Maekawa dojo only show up on days Kaoru instructs. Word Of God also states that Kaoru is a very powerful fighter, but she often gets overshadowed by Kenshin and Sano.
Big Lipped Alligator Moment: In the big battle of The Movie, Sanosuke goes against The Brute for an awfully-drawn-out battle... leading to him calling a timeout. They both stop. And eat. Until The Brute turns out to be a vegetarian who doesn't take kindly to Sanosuke tearing into that roast chicken. He has no problem sharing the booze, though...
Complete Monster: You think they can't make Jin-e and Kanryu worse than their original incarnations. As shown by Jin-e's murder rampages that will make Takashi Miike proud and Kanryu's blackly-comic atrocities (ranging from petty to downright callous), we thought wrong.