If you're looking for manga similar to Rurouni Kenshin: Yahiko no Sakabatou, you might like these titles.
Souzou Sagara, the commander of the Sekiho Army, is determined to overthrow the new government and change Japan. A young boy called Heihachi admires Sagara, and is determined to help him lead the country towards change.
In the age of strife and suffering, justice and righteousness are but impractical concepts. Onden, a travelling monk, fearless and wise. He despises the lies brought about by mediocre interpretations of justice and righteousness and wishes to set things right and guide the masses to be truthful to themselves.