Reason for buses vs trains is the they go to the center of town.
You have 2 1/2 days in Florence and want to use one of them to leave? Have you spent time in Florence before as otherwise it seems a bit of a rushed trip. If you have already "done" Florence then why not train to Siena and spend your time there? We adore Siena but as with Venice, a day trip does not show it in its best light as you can be shoulder to shoulder with tour groups.