Ideals and Ruroken
Rurouni Kenshin is, when you get right down to it, about a bunch of idealists fighting to uphold their own principles. Much of the story would not have happened had any of the characters been less passionate about their ideals. Let's start with Kenshin, with his ideal of a world in which swords (and swordsmen) are not needed. Or Kaoru, with her vision of kenjutsu as a means only to protect, rather than to do harm. Or even Shishio, who thought of the perfect world where might is truly right, and the way of the strongest is the way of all -- indeed, a much more simple and less abstract vision than those of the former two. For Kenshin and Shishio, these ideals would lead them down completely opposite though unavoidably convergent paths.
In Kenshin's case, his idealism was the main reason for his resulting confusion and violence. We have to remember that, unlike what the English title implied, Kenshin was not ever a samurai. He was of peasant stock, and it is doubtful if, before meeting Hiko, he had ever been taught the way of the samurai. The loyalty to his lord, readiness to die, and unquestioning -- even blind -- obedience to his superiors had not been drilled into him. Perhaps what the triumvirate (specifically, Katsura Kogoro) had expected in hiring him was a ready and willing killing machine. They couldn't have been more wrong.
What the Ishin Shishi needed was someone who would kill for them without question, who would serve their end without thinking twice about the means. Shishio Makoto fit this role perfectly later, but Himura Kenshin, with the principles taught to him by his master, and his own desire to ease the people's suffering, was faced with a major moral dilemma as he tried to reconcile his own ideals with that of the Ishin Shishi's demands. Kenshin had abandoned his training to help the people, and while perhaps at first he could think of reasons why he had to kill, it probably eventually became too much, as the murders became -- to him -- increasingly senseless. The more he killed, the more he lost sight of his original intent, and perhaps it was that which weighed heavily in his heart.
The Hiten Mitsurugi Ryu that Hiko Seijuurou had taught Kenshin was certainly stronger than most of the other schools of kenjutsu -- perhaps even the strongest of them all -- but it was not meant to be bound to a single party or cause. This is perhaps why only one master and one student exist at a time. Again, the reason for this is deeply rooted in the idealism of the original Hiko Seijuurou (the name is passed down from master to student). The Hiten Mitsurugi Ryu was meant to be used by one person to help the other people suffering around him, one by one, person by person. It was not intended to be used to change the world or start revolutions, simply because it was too powerful and, in the hands of fanatics or revolutionaries intent on the end rather than the means, it would become simply another killing tool. Eventually, it could even be used to convert people to an ideology by force or out of fear.
When confronted with Kiyosato, the common soldier who had wanted to live so badly that he managed to wound Kenshin (the first slash in the cross-shaped scar), Kenshin began to realize just how far he had strayed from his path, and his struggle to get back on track would take him over a decade.
And then there was Shishio. Shishio was the antithesis of Kenshin. Apart from their skill in swordsmanship, they were polar opposites. One believed in an ideal of peace and equality and would willingly have died for it, while the other believed that man's very nature was violence and greed and would have happily killed to prove it. It's a very interesting contrast which formed the heart of the conflict between the two.
Seta Soujirou, on the other hand, seems to me to have refused any kind of ideal coming from someone other Shishio himself. I think that, unlike Shishio, Sou didn't really believe the "flesh of the weak, food of the strong" mantra that Shishio kept trying to drill into people. I think that Soujirou in fact believed that the strong were supposed to protect the weak. However, due to his traumatic childhood, he grew to reject this belief quite violently, choosing instead to embrace Shishio's because the proof of it was right in front of him. I don't think Soujirou would have been so shattered by the abuse he had endured had he not had some deep-seated hope that there was someone supposed to save him. This is evident after his battle with Kenshin. Anyway, I'll talk more about Soujirou in Saviour.
Looking at the characters in RuroKen, even the villains, I can't say for certain if any of them were truly, crazily evil. All of them felt that their deeds were fully justified or reasonable -- except for Shishio, who acted out of a base, self-centered view of the world (maybe that's why he wound up in hell) and was bad to the core, and Usui and Jineh (remorseless killing machines). All of them held ideals and principles (of a kind), and Kenshin himself is often reluctant to say which of them is wrong or right.