Nagasaki is great. I recommend three days and spending a half day on the tour to Gunkanjima Island with Gunkanjima Concierge company. Other companies do the tours but Gunkanjima Concierge gives you an English audio headset. Also, I was booked with another company that prematurely canceled two days of trips due to bad weather forecast, Gunkanjima Concierge only canceled the first day and I joined their tour on the second day.

I stayed at the JR Kyushu hotel in Nagasaki connected to the train station, very convenient.