You need to make some compromise among when, where and what.
This is a honeymoon trip. So, you would not want to change the dates, wouldn't you?
If you fix the place to be Hokkaido, you could not do some of the things you want to. Snow would be OK in Asahikawa. The mean snow falls in November is 107 cm in Asahikawa. However, the penguin march would be held officially from 10 Dec last year in Asahiyama Zoo. Hot air balloon is OK near Yorkshire farm in Sahoro, but it may require Japanese. Some ski resorts would be opened until then, but Sahoro opened on 1 Dec 2016 and Tomamu on 26 Nov 2016. Snow monkeys are in Nagano. Hakodate ones are from 1 Dec. Onsens are everywhere. Noboribetsu would be the best in Hokkaido. There are many shopping sites. Fruit picking is until early November in Hokkaido. Flower does not bloom in November in Hokkaido. Basically, the autumn - winter transition is over in early November in Hokkaido. Rather, you may focus on top sites in this season in Hokkaido.
If you start from the activities, you may be better to change or add the destinations. Snow and flowers could exit in May in Hokkaido. So, there could be some answer in the southern hemisphere, say, New Zealand. Or, ever-spring countries in the Andes in South America. In Japan, you could compensate Hokkaido with the southern cities. If you add Tokyo, you could do snow monkeys in Nagano. Fruit picking, flowers, and autumn leaves are possible in Tokyo in November. If you focus on the activities, the itinerary could be much different from one of the representative ones. This one below targets on snow monkeys and East Hokkaido.
https://www.martinbaileyphotography.com/japan-snow-monkeys-and-hokkaid...So, you have to decide your standing point at first. Hokkaido, plus Tokyo, or somewhere not in Japan. Season top sites, similar to the famous route, or activity oriented one.
For your info, here is a kind of seasonality index in your sited destinations.
+1 Chitose
+ The last minute shopping
http://www.outlet-rera.com/english/-3 Hakodate
- Monkeys from 1 Dec
http://www.hakodate.travel/en/things-to-do/top7/yunokawa/ http://www.hako-eco.com/map.html- Hakodate Christmas Fantasy from 1 Dec 2016
http://www.hakodatexmas.com/- Goryokaku Tower Illumination from 1 Dec 2016
http://illumi.walkerplus.com/detail/ar0101e17351/+2 Lake Toya
+ Toyako Illumination Street from 1 Nov 2016
http://illumi.walkerplus.com/detail/ar0101e17347/+ Toyako Illumination Tunnel from 14 Nov
http://jp.zekkeijapan.com/spot/index/269/?language=ja+3 Noboribetsu
+ A penguin parade at Noboribetsu Marine Park Nixe
https://www.nixe.co.jp/pdf/leaflet_eng.pdf https://www.nixe.co.jp/nixe-hiroba/#penguin+ The best onsen in Hokkaido
+ Salmon run in Uyoro River in Shiraoi near Noboribestu
http://kandonotoki.jp/detail-ID=00061.php https://en.wikipedia.org/wiki/Salmon_run-1 Asahikawa
+ Mean snow falls in November is 107 cm.
- The penguin march at Asahiyama Zoo was held officially from 10 Dec in 2016.
http://www.city.asahikawa.hokkaido.jp/asahiyamazoo/event/d0550178212.h...- Asahikawa Machiakari Illuminations from 3 Dec 2016
http://www.atca.jp/machiakari/+1 Biei
+ Blue Pond/Shirohige Falls Illumination from 1 Nov 2016
https://trip-s.world/hokkaido-biei-blue-pond+1 Furano
+ Furano Ski Resort opened on 19 Nov 2016.
http://www.princehotels.co.jp/ski/furano/+-0 Yorkshire farm / Sahoro
+ A hot air balloon in November
http://h-takarajima.com/modules/waffle0/index.php?HypEncHint=%E3%81%B7... http://h-takarajima.com/modules/waffle0/index.php?HypEncHint=%E3%81%B7...- Sahoro Ski Resort opened on 1 Dec 2016.
http://www.sahoro.co.jp/+1 Tomamu
+ Tomamu Ski Resort opened on 26 Nov 2016.
+8 Sapporo
+ Sapporo Kokusai Ski Resort opened on 18 Nov 2016.
https://www.sapporo-kokusai.jp/+ Snow Cruise Onze Ski Resort opened on 18 Nov 2016.
http://www.onze.jp/+ Teine Ski Resort opened on 19 Nov 2016.
http://www.sapporo-teine.com/snow/+ Shiroi Koibito Park Illumination from 3 Nov 2016
http://illumi.walkerplus.com/detail/ar0101e17342/+ Sapporo Factory Christmas from 3 Nov 2016
http://illumi.walkerplus.com/detail/ar0101e17327/+ Moiwa Shalom Church Illumination & Christmas Trees from 5 Nov 2016
http://illumi.walkerplus.com/detail/ar0101e17336/+ Sapporo White Illumination from 24 Nov 2017
http://white-illumination.jp/+ German Christmas Market in Sapporo from 25 Nov 2016
http://www.sapporo-christmas.com/index.html+2 Otaru
+ Kiroro Ski Resort opened on 27 Nov 2016.
https://www.kiroro.co.jp/ja/+ Yoichi/Otaru Snow Story from 12 Nov 2016.
http://www.otarusnowstory.com/
