Having just traveled in this area last month, I would say that Siena can easily be seen in a day. If you have extra time on your hands, I would think that time would be best spent in Florence -- we spent 4 full days in Florence.

(However, the hotels might be significantly more in Florence, which might tips the scales towards spending the night in Florence.)

I do not think you can combine Sienna and Pisa in one day, especially if trying to navigate all of that by train.

Instead, I would suggest that you take a morning train from Florence to Pisa (70 mins). There's really not much more to see than the Tower/Duomo complex. (We arrived by train at 9:30 am, walked to the Tower, bought our tickets right away ... and were given an entrance time of 2 hours!) Then, for the rest of the day, we took a 20-min train to Lucca; there was a heck of a lot more to do and see in Lucca than anything else in Pisa. Lucca was a charming city!