I travel to/from Berlin everty year. A very welcoming city, IMO. The underground is complicated but I am not sure I would be taking the Big Bus tour to see all the tourist attractions? Why not taxis? Or, rely on your hotel concierge? The balance of your itinerary makes a lot of sense. I like Bruges, I love Amsterdam. PM me if you want more detailed LM advice on where to stay in both BER & AMS.