I have no idea if I would prefer Pisa, I've never been there. I know that I loved the beauty of the pretty much all Gothic architecture of Siena. Other than Pisa has a tower that hasn't finished falling yet, I know nothing of it. But then I knew nothing of Siena before I went there for a meeting and then didn't have time to explore or visit museums. Feel free to encourage me one direction or the other, or try to get me to do both, if I've been working hard enough to justify two days off, and you are staying somewhere with floor space for an extra person...