We were charmed by Gion on our last visit. I would welcome some recommendations for other charming villages or areas where there are still old houses and/or interesting historical areas. Preferably less well known. This sounds a bit vague for which I apologise!

I understand why most travelers want lesser-known places. Maybe you've already been to the famous attractions in Kyoto or you want a more peaceful tour.

You may want to visit Shirakawa-go and Gokayama (Gifu) - or Ogimachi (Gifu).

Thank you.

This link lists multiple categories (geisha, post towns, ...) of old style districts. The place names are links.
Historic towns and districts in Japan (japan-guide.com)

Kawagoe in Saitama Prefecture - Nicknamed "Little Edo", Kawagoe has many preserved warehouse buildings, traditional storehouses, and Kurazukuri wooden houses lining its main street. Kawagoe is close to Tokyo, however if you're willing to go farther, I would recommend Kakunodate in Akita Prefecture. Kakunodate is a former samurai town has many well-preserved samurai residences, merchant houses, and storehouse buildings from the Edo period.