One WMG revolved around why Shishio was laughing as he combusted. Just figured it out upon re-watching the series: Shishio's wish was for Japan to become militaristic and expand into the world, right? Kenshin thought he was going to stop that from happening if he defeated Shishio - and then what did Japan end up doing anyway?
Paraphrasing a Fridge Brilliance I found on the Martial Pacifist page: Shishio is stated to only have 15 minutes to fight before he combusts. The reason is that it is "'the era' choosing who would be victorious—i.e. the world moving into an age where Kenshin's beliefs about protecting the weak have more bearing than Shishio's 'the victor is right by default' stance". Time chooses the victor, not swordplay(and also, allows Kenshin to avoid breaking his "thou shall not kill" philosophy).
From the Trust and Betrayal OVA, near the end when Kenshin is limping along using his sword for a crutch the sword can be heard making some metallic sounds. This turns out to be the sound of loose pins within the handle, indicating just how out of practice Kenshin had been (thus not maintaining the sword) and emphasizing the desperateness of the situation.
Also, the pin being loose in the reverse-blade sword is actually a plot point in the manga, as it was supposed to be a sign of how the sword was designed to blunt its own force so that it would never kill. Because no one ever died of being hit with a thin metal stick of extraordinary hardness.
At one point, when Okubo asks Kenshin to kill Shishio, some of the Kenshin-gumi wonder if Kenshin would have been executed after the Bakumatsu if he hadn't vanished, which is what happened to his real life counterpart.
After taking some proper kenjitsu classes, the name 'Battousai' gained a new significance. A battou is a move you do by drawing the sword really fast- in other words, it's an opening move. He didn't get the name because he was so much better at doing battou's compared to everything else; he just happened to kill his opponents that fast. Zashiki-Warashi
Many people point at Saito's claim of having given up drinking as being a change that Watsuki made, since the real Saito was known to be a drinker until he died. However, the same scene where he says that he's given up (or is just cutting back) on drinking, Saito also says that drinking tends to make him want to kill. Being that he was in the middle of an undercover investigation of dirty politicians, (who would certainly fall under Aku Soku Zan, and whom Saito did later go back to kill off) the drinking thing is probably a polite lie that Saito made up just so he wouldn't jump the gun and blow his investigation.
While the live-action film is chock full of merits, one thing might get the attention of those who closely watched the anime: Saito, instead of working for Okubo Toshimichi (a powerful yet statesman-like Meiji government leader), he was made one of the direct subordinates to Army Chief Yamagata Aritomo (a known military commander and war-hawk in the Meiji and Taisho period). While both were portrayed as benevolent bosses in the anime, General Yamagata was known in real life to harbor anti-democratic and expansionary sentiments. Considering that Yamagata's policies would pave the way for Showa-era Japan's military expansion in Asia, it was probably quite appropriate that Saito, the series' Knight Templar by virtue of his Shinsengumi track record, would side with him.
It used to bother me that Sanosuke was considered the hand-to-hand combat expert of the series, despite there being at least a few characters were far more skilled. But I realized that first and foremost, Sanosuke was a street fighter. His fighting style was less about unarmed combat martial arts and more about fighting his own way with his two fists. While his refusal to follow Saitou's advice could be chalked up to stubborn ignorance, it fits his character and signifies the contrast of finding your own way and fighting style.
Shishio's No Sell nature of being able to counter techniques after seeing them once can serve a few purposes. It's a nice contrast to Kenshin's own Awesomeness by Analysis fighting style; while Kenshin usually has to find clever ways to defeat techniques, Shishio can simply catch the opponent's blade or come prepared.
Secondly, it provides a good justification for how he easily defeated Saitou, Sanosuke, and Aoshi. While it could simply be attributed to being just that Badass, he already had knowledge of all three of his opponents techniques: He blocked off Saitou's gatotsu with his headband, and since Saitou's gatotsu is merely a set of variations was able to counter it. With Sanosuke, he already had knowledge of Anji's techniques and knew he could merely take the hit. And he had already tested Aoshi with four of his mooks.
IIRC, they were fighting in a small arena inside a mountain in late 19th century Japan. The giant torches might have just been for light, and I'm fairly certain that Kenshin said that they were flaring up so much as a reaction to Shishio's ki, like how Kenshin's ki causes leaves to split as they pass by. Of course, since they were doing this in said arena inside a mountain, I guess it might also create the leaves in the first place...
On a related note, how is he able to have sex with Yumi without overheating? (Or cauterizing her vagina shut?)
Meta example. Hannya's original back story would've had him naturally deformed, which turned him into an outcast. This was changed because (according to the author at least), he had a talk about it with the editor and they concluded that it's too dark and needs to be changed. If that was too dark, what about Sojiro's back story?
It wasn't that it was too dark; it was that he didn't like the message that a person's fate can be decided from birth.
One of the WMG asks what kind of training Kenshin still needed given the fact that he only needed to learn kuzuryusen and the secret to acquire the complete set of hiten moves. It hit me that although Kenshin was a kenjutsu virtuso, he was not a great tactician and was still naive and immature. Samurai in training not only learn kenjutsu but bushido (the philosophy of the sword) and most likely tactics to successfully fight and win on the battlefield. Kenshin's fighting style relies on using his innate reaction ability along with hiten moves to defeat his opponents, something his master exploits with his training. Although Kenshin is a powerful fighter, he is not a cunning one and relies too much on his innate abilities to win which is why Hiko calls him his "stupid apprentice."
You must also remember that Kenshin was never a samurai and thus never trained in Bushido. It's probably safe to assume that most Hiten successors were not samurai, since Hiko implies in the OVA and in the manga (iirc) that the Hiten sword was typically a sword for hire.
Has anyone ever thought much about the Kaoru doll and that it was made in her EXACT LIKELINESS, right down to the intimate details? Looks like Gein'sbeen up to something...
How familiar would anyone who examined the body have been with Kaoru's intimate details?
Considering the one who examined Kaoru's "body" was Megumi, a doctor, she would have been familiar with anatomy. It's also safe to assume an autopsy was not performed considering the big reveal had to be instigated by Aoshi.
A small hint but made clearer in the live-action movie. With Japan's strict Last Name Basis, and Kanryuu calling Megumi just "Megumi". Her family was killed, and her being the only survivor. Also his yes-men call her only Megumi. Could this perhaps mean that they... gang raped her?