the downsides first: they have strict "lights out" policies and the temple gates often close at around 8, so you can't stay out late. also, the baths and toilets are shared, and are often traditional-style if you know what i mean. but they aren't really huge problems if you're only staying one night, and are easily outweighed by the positives: gorgeous gardens that you won't see anywhere else, and a unique and very authentic experience of the country's buddhist tradition.
this time, we stayed at "myorenge-in" in ohara. it's a bit hard to get to, but the location is one of its key assets: right behind the famous "sanzenin" temple known for its mossy gardens.
but i would say the best part of staying here was the food.
below: breakfast and dinner, both vegetarian meals, at myorenge-in