Itinerary Advice Wanted: Kyoto-Hakone-Nikko-Tokyo; late September, early October

I want to visit Kyoto at some point and will depart from Tokyo at the end of my trip, thus I thought it makes sense to fly into Kansai airport (Osaka) to start my trip with Kyoto. Do you agree, or would you fly into HND (if cost is not an issue.)

Too busy of a schedule? Change the order of anything? Skip/swap any destinations? If weather causes delays, what would you eliminate first?

I appreciate some quiet/peaceful time. Nature and culture are my priorities over shopping and eating, but I hope to get some of that in Tokyo:).

Thank you for any and all advice!!!

6:55pm Tuesday
Arrive at Kansai airport (Osaka)
Tuesday night
Plane arrives 7pm
8:16pm Limited Express Train, Haruka -54 (for Yasu)
9:32pm Arrive Kyoto Station
Take 18 minute Bus & 1-4 minute walk to Gion/hotel
\~10pm Hotel check-in
Wednesday
Explore Kyoto/Rest
Spend 2nd night at Kyoto Inn
Thursday
Explore Kyoto
Train to Hakone
Overnight in Hakone; Onsen
Friday
Hakone: Lake Ashinoko hike and/or cruise w/ views of Mt Fuji
Train to Nikko
Overnight in Nikko
Saturday
Nikko: visit Tosho-Gu; maybe see waterfalls
Train to Tokyo
Overnight in Tokyo
Sunday, Monday, Tuesday, Wednesday
Explore Tokyo (w/ my brother who will be there for work)
6:35pm Wednesday
Depart from Haneda airport

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