Rurouni Kenshin/WMG

Sojiro was a stronger fighter than Shishio
The only reason Sojiro lost his fight was because he was having a mental breakdown at the time. If memory serves, despite rushing at near full speed into Kenshin's "Hit-Them-Nine-Places-At-Lightspeed" attack, he was still able to get behind Kenshin and slash him across the back. Sojiro was surprised that it didn't kill Kenshin. Had he been at his normal best, the series would have ended there. Shishio, although he had the charisma/people skills necessary to lead his band of evildoers, had to use the fact that his opponents were very weakened (Sano breaking his fist on him), hidden armor ("Thank God I walk around with a thick metal plate on my forehead"), and a bunch explosion/fire themed weapons. All Sojiro had was a high-quality sword; his speed was all he needed. Also, it should be noted, he didn't have a time limit. Even though he supposedly believed that the stronger should dominate/kill the weaker, Sojiro either never let himself realize his superiority, or made an "exception" for him.
 * However, Shishio seems to be a lot more durable than Sojiro. Admittedly, all the people he was fighting were exhausted, but he still took all their ultimate techniques, then every single one of Kenshin's techniques and his not-quite-ultimate-but-still-extremely-powerful technique on par with the best techniques of the others. Plus, he was a lot more experienced than Sojiro and could instantly find anybody's weakness just by watching them fight.

Kenshin is sterile
It's a well established fact that Kenshin carries a reverse blade sword. As a tool, a swords function is to kill. So a sword that can't kill is basically a sword that doesn't work. And since we all know that swords are phallic symbols, then it's pretty safe to conclude that if Kenshin's sword doesn't work then his... um... "sword doesn't work."
 * Jossed by the Distant Finale - there's just about no way Kenji's not Kenshin's kid.
 * They never explicitly say that Kenji is Kenshin's son. Just because he looks like Kenshin, and had Kaoru as a mother, and Kenshin said that he'd have to inherit the sword from Yahiko doesn't mean that he's Kenshin's son. Also ignore the part where the action bubble says that Kenji dislikes his daddy as he pulls on Kenshin's hair.
 * It DOES say that Kenji hates his daddy in one of the final chapters when he's pulling on Kenshin's hair. So it's not unreasonable to say that Kenshin is Kenji's biological daddy. Of course, it could ALSO be that Kenji hates Kenshin because Kenshin isn't Kenji's daddy...

[[WMG:Gein faked He does mention someothing about someothing that has both beauty and functionality right?it was his own doll,which

Kenshin is a descendant of Nanashi
It's fairly obvious that Sword of the Stranger is set long before Rurouni Kenshin. Both Kenshin and Nanashi are jaw droppingly good swordsmen (although Kenshin has outdone his ancestor), both feel guilt over bloody pasts and carry "useless" swords because of it, and  You don't have to stretch your imagination to see it.

Kenshin is a descendant of Inuyasha and Kagome.
His resilience and and strength are lingering demonic abilities.
 * That might also explain his red hair, which is unusual for Japan...

Kenshin and Kurama are the same person
Long red hair. Big eyes. A lot older than he looks. Seems friendly and sweet, until you see him in a fight.
 * At one point during the Dark Tournament, someone leaves a nice cross shaped scar on Kurama's face.

Aoshi (with or without Misao) is the ancestor of Seto and Mokuba Kaiba
Though the resemblance shows up more in Seto than Mokuba. Think about it. Tall, sharp features, penetrating stare, Jerkass personality... they even have similar haircuts. And when Aoshi is defeated by his rival, he goes off to brood, just as Seto did after being defeated by Yuugi. And then there's the trench coats...
 * Well, Misao can be pretty cruel at times (mainly if her victims are called Sanosuke Sagara and Yahiko Myoujin)... Not as much as Manga!Mokuba, but yet...

Kaoru is the daughter of Souji Okita and Sei Kamiya from Kaze Hikaru
She was adopted by missing, surviving members of the Kamiya family. Saito didn't recognize her because Sei had her in secret and he never found out about her, and she fell though some time hole in her early childhood which explains why she's older than she should be.
 * Sorry dude, Kaoru's dad is named Kamiya Koshijiro, said by a master of some dojo in the manga, also, in one of the pilot chapters,
 * The pilot chapters diverge from the series canon. She could have been adopted by Koshijiro who could be a distant relative of Sei's. Situations like those were really common back then. Besides, they never mention her mother in the series, do they? (And even if they did, it could have been Koshijiro's wife, not necessarily her biological mother). It would also explain why she looks like Souji and her personality is like Sei's.

Rurouni Kenshin takes place in the Marvel Universe.
Apart from some character designs being clear Shout Outs to Marvel characters, some characters do have clearly superhuman abilities that don't seem like Charles Atlas Superpowers. Sano, Sojirou and Enishi have clearly demonstrated superpowers, and their powers appeared right after incredibly traumatizing events, similar to many mutants. As to why Jin-E was the only person in centuries to master his particular style's ultimate technique, well, the reason is that the founder was a mutant who could hypnotize people, and Jin-E is another mutant who has hypnosis-related abilities.
 * Well, the creator is a big fan of Marvel, so that makes sense.

Shishio is Captain Aizen.
Think about it. Disregarding the part where Shishio meets Yumi and Houji in hell, we have the fact that: 1. We see his unburned face once or twice, and he is shown to be quite handsome; 2. Shishio was a planner, always trying to deceive his opponents and predict their next moves; and 3. He's arrogant and quite the Magnificent Bastard, always being supremely confident in his own capabilities. So what about Aizen? He's 1. Quite handsome; 2. A planner, constantly deceiving his enemies (and allies!), and easily predicting the main cast's next moves; and 3. He's arrogant and a Magnificent Bastard. Heck, he even got a Shikai that helps him deceive people! His previous life as Shishio gave him extremely good swordsmanship skills, allowing him to take down other Shinigami using their Shikais and Bankais with ease. He simply changed his name to allow him to go incognito (plausible, seeing as how we never saw a way of keeping track of the people in Soul Society).
 * This one would just like to state that it would sorta be kinda ironic if true given the fact that the head Captain of the Gotai 13 uses fire based abilities, like Shishio. This one would also like to state that the idea of Shishio and Aizen being the same person scares the ever living crap out of me. Just try and imagine a merging of Shioshio and Aizen's abilities and that would probably be Aizes Bankai. Have fun trying to sleep tonight!

The story takes place in the same world as [Kenichi:TheMightiestDiscipleKenichi: The Mightiest Disciple]
Seriously,they both have charles atlas superpowers far beyong the level of possibility,moral differences of the < >type,in both series most of the truly strong villains,even some complete monsters have honor(in both there are exceptions) and both of them have a history that fits our world,while some things are hidden.Whether Shisio was the creator of Yami or (most probably)if he is a member who modeled the Juppongatana after it,I leave it to your debate(through for that to be correct,the armed division should be similar to the unarmed division in terms of leadership,and that is another wmg altogether)