Bilbao, crossed by a river, WAS and industrial city that, when the steel factories and the shipyards closed or moved out of the city, reinvented itself and transformed all the river area. No industrial grit at all anywhere in the city (I wonder where this idea comes from, maybe from old publications?), it´s the 2nd cleanest city in Spain after Oviedo, the highest index of happiness in Spain and the fourth most walkable city in Europe. "Bizarre" architecture can only refer to the Guggenheim museum, as we have a 14th-15th century beautiful old town, classic architecture all over the city, and then modern architecture in the renewed part of the city, by 7 Pritzker prize (the Nobel of architecture) architects. Opera house (6 operas per season), concerts, surrounded by green mountains, a 1915 funicular, and 9 miles to the coast. You can get on foot practically anywhere in the city. National Geographic has chosen Bilbao as the city with the highest quality of life in Spain, https://www.bizkaiatalent.eus/en/pais-vasco-te-espera/conocenos/national-geographic-mejor-ciudad/.
Donostia-San Sebastian is a "postcard" city, but also a working city, the Basque Country´s income comes mainly from making trains, car components, Mercedes vans, satellites, biosciences...33% of our GDP while tourism is barely a 7%. Beautiful setting, smaller than Bilbao (190,000h vs 345,000h), classy, and while D-SS is considered the gastronomic capital of Europe, Bilbao is very close to it, offering very similar gastronomy. Both are very clean, rainy and safe.
Of course, as I´m Bilbao-born, I´m biased, but if you read updated information, it may all be true...
TRAINS: Spain offers many types for trains, from the AVE high-speed ones to the standard wide-gauge ones and the small narrow-gauge ones. You need to know which one you want to take and where, because in some cases (like the trip from Bilbao to D-SS or viceversa) the bus is the logical option. Not all trains are identical.