In addition to size and proximity to the mountains, a third difference between Bolzano and Ortisei is the probable temperature in September. Bolzano is a valley city and subject to the same sort of heat you might encounter in Verona/Padua/Venice, etc. Unfortunately, many of the city's hotels are not air-conditioned. Once you get up into the mountains you won't need air conditioning.
I do like Bolzano. It has a good-sized and very pretty historic district, lots of restaurants, and a number of museums, including the one housing the Iceman. It's worth a visit for sure. Buses to the mountain towns stop very near the train station. From there it's not a long walk to the historic center. Bolzano would be a great place to go if you are unlucky with the weather one day.
Bressanone is a smaller valley city, also with a pretty historic district, but it doesn't match Bolzano's museums and the train station is a healthy walk for the center of the historic district. And its hotels are equally averse to air conditioning.