Depending where you want to go I guess but here are my opinion for base and possible destination from it (base of my experience last trip and my research etc):
My proposed itinerary is probably clockwise or anti-clockwise of the following (just adjust as needed):
- Membatsu Airport (Abashiri)
- Abashiri
- Train (Norokko, not sure if they run during Autumn tho) to Shiretoko-Shari
- Either Stay at Shiretoko-Shari or bus to Utoro to access to Shiretoko National Park etc
- Bus to Shiretoko-Shari, Train (might have SL train from Shibecha) , to Kawayu for Akan?
- Akan
http://japan-guide.com/e/e6805.html- Train/Bus/Drive to Kushiro
- Kushiro
- Travel to Nemuro?
- Train To Obihiro (the last remaining Banba race in Hokkaido I believe)
- Train to Asahikawa (use as base? for Daisetsuzan, Furano, Biei etc)
So pretty much:
1. Utoro as base for Shiretoko National Park
2. Kushiro as base for Tancho Park, Akan, Nemuro
3. Obihiro/Tokacchi as base for Furano/Biei etc
4. Asahikawa for Furano/Biei/Daisetsuzan etc
We stayed at http://shiretoko.co.jp/ last trip, definitely one of our better stay though our room is pricey, open air private onsen facing ocean. Though, there are many hotel in those surroundings.
Asahikawa, we stayed at Asahikawa Grand Hotel, though I won't recommend it as it is some distance away from the station, though it is more lenient with the check in time.. We were there early (as usual, to drop bags) at around noon, and were allowed to check in, definitely one of the rare hotel I had encountered that allow early check in. The hotel is posh but a little old unfortunately..
Abashiri do not have much selection, easiest will be Abashiri Toyoko Inn or Central Hotel.
Akan has many ryokan too, in face, I think they have many traditional ryokan too but can be pricey...
I had included Kushiro and Obihiro in my first plan but unfortunately had to scrap it due to time restraint so I do not have much personal experience here..