Vacation to Japan Review: Kyoto, Ryokan Accommodations, Hakone, Culture & Beauty

Trip was great overall. However, we do this kind of thing all the time (we are experienced travelers), and I think this travel company should have been a little bit more communicative about the itinerary.
(1) we really liked the matchiya experience except for that we were 5 people (two families) with one bathroom. We had numerous conversations about two bathrooms in the context of a different situation.  Agent should have known this  was going to be an issue for us. 
(2) the Kyoto hotel stairway was very steep and dangerous to use with the lights out in the middle of the night.  If there was a second bathroom, this would have been less of an issue
(3) the Kyoto hotel was very loud. It was literally impossible to sleep.  There should have been some kind of sound machine/white noise in there.  Or, some other solution. 
Green Hotel was a bit tired.  The rooms, and even the dining hall. The tables had plastic table cloths on them. Very old school. And, the only way to use any of the facilities was totally nude and gender-specific. No other alternatives. This should have been discussed a bit more. Americans are uptight.
Same kind of thing at the Ryokan.  My son did a "no fish" dinner. Agent should have also specified "cooked".  He was given raw chicken and we were afraid for him to eat it. Agent should have gone the extra mile and realized that raw chicken would be an issue for an American.  Last, Ryokan was in an odd location and it was dangerous to walk around on foot. No sidewalks or anything like that.  Cable car was shut down and you couldn't see the mountain at all (from any vantage point). Perhaps Mt. Fuji should have been planned a bit better.