I’d definitely recommend the Hotel Indigo Nagasaki.

It’s a genuinely charming property — beautifully designed, calm, and surrounded by greenery.

In terms of location, both the Indigo and the Crowne Plaza are actually quite close to each other, just on opposite sides of Glover Garden.

I haven’t stayed at the Crowne Plaza, but from the look of the building and internet site photos, it seems like a rather dated, characterless hotel, whereas the Indigo has real personality and a much warmer atmosphere.

I travelled entirely by Shinkansen during my one-month trip last August, and it really is the best way to get around Japan — fast, effortless, and very reliable, even with luggage (and as any frequent flyer, I travel light).

So I wouldn’t let the train connection put you off. Take a good book, watch the scenery unfold through the window, and enjoy the journey.