I can't remember him showing up at all after the Kyoto Arc in the manga.

Even when something happens to Kenshin he doesn't come to snap him out of it.

He was just too strong of a character, they couldn't use him cause he could just show up and beat the crap out of the current bad guy with ease.


As for Kimimaro being on the Sannin level....I think you might be giving him too much credit there, but we will see.