Sure be some Trolls out tonight.
Try a 2006 Internet Anime produced by Sunrise called Bakumatsu Kikansetsu Irohanihoheto. Set in the same time period as Kenshin (Following the end of the Edo era when the Americans were enforcing their ideals on the weakened state of Japan), it is 'Historical Fiction' and pretty good. Near the middle of it, it starts to slide more towards Spirits, extreme crazy fighting and lol, Japanese Revolver Ocelot shooting people from 2 miles away off rooftops. But still, the show is well animated, interesting storyline and somewhat good character development. And its got Inoue Kazuhiko so what more could you want?
As for other straight Ninja or Samurai shows, sorry, I can't suggest some. I don't go for shows based on themes. I just go for shows based on if they have good characters, concepts, writing and flow.