11 days in Hokkaido and Kyushu – Itinerary advice

Planning on a trip to Japan on the beginning of September, and I’d like some advice on the followings:
1. Recommendations on things worth doing in this season (anything from culture, food, shopping, museums and experiences, hot springs, nature (easy hikes)).
2. A nice, not so expensive place to stay in Hokkaido with natural hot springs that allows men and women to bath together in bathing suits.
3. A nice not so expensive place to stay at the south island, to be relatively close to things (we really have no idea where to stay). Is it hard to get by in public transportation? Should we rent a car?

Thank you

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