What do you think of our rough itinerary?
As a whole I like it. Particularly you will stay long in Kyoto, which is very nice.How do you recommend we fill our days? And what do you think about the hotels we booked?
You choose middle range "business hotels" with rather good reviews.
Personally I think Kinosaki onsen for two nights is not bad, but if you want to experience genuine onsen experience you might better have dinner (and breakfast of course) at onsen ryokan. You should be there around 15:00, get into the room, have tea and small sweets provided in your room, then wear Japanese bath wear (Yukata) and then go to Onsen bath. Onsen hotel is not cheap, so you might better enjoy the stay itself. Normally Japanese tourists go at least three times to the onsen bath (at the time of arrival, after dinner and before breakfast). Of course you can take 7 times (at arrival, before dinner, after dinner, before sleep, at midnight, before breakfast, after breakfast :). Therefore, Onsen is rather hard work :). According to your itinerary, you will go to Himeji castle after onsen, which might be tiring.
Below is my comment to your itinerary.02.10.2019: Kinosaki Onsen; Kinsui Annex
03.10.2019: Kinosaki Onsen; Kinsui Annex
Does this include meal? i recommend to include meals. As I searched on the net, international booking sites tend not introduce meal plan, so you might better check Japan-based booking site such as Rakuten.https://travel.rakuten.com
Half board (dinner and breakfast included) is expensive so you might better stay only one night and then start afternoon to go to Himeji and stay there (Himeji castle next day).07.10.2019: Naoshima; Daiwa Roynet Hotel Hiroshima
After Naoshima you may go to an opposite direction to Nagoya and stay there. Nagoya is not that interesting but at least there are many reasonably priced hotels around the Shinkansen station. And you can go to Takayama early in the morning to enjoy nice scenery from the train.08.10.2019: Kanazawa; Hotel Pacific Kanazawa
Instead of Kanazawa you may better go to Takayama and sightsee on this day. The scenery from train is better for Nagoya to Takayama than Kyoto to Kanazawa.09.10.2019: Shirakawa-go & Gokayama (day trip); Hotel Pacific Kanazawa
10.10.2019: Takayama and late check-in in Tokyo; ICI HOTEL Asakusabashi by RELIEF
On 10th, you can sightsee Kanazawa before going to Tokyo in late evening. It will take about 2.5 hours from Kanazawa to Tokyo by Shinkansen.
Of course I think you have considered Japan Rail Pass 14 days which will pay off for your itinerary.