Use Florence as a base for day trips or stay in Siena?

I would decide based on the ease of public transportation, if that's what you're using. It would be nice to see some of the smaller towns, especially those isolated with a view. But that's really hard without a car or an organized tour. You have listed some of the best big towns, and I agree that Siena and Lucca are really nice. Both also worth sleeping in.

It's hard work, but I'd suggest looking at bus schedules from Siena and Lucca to see if you can easily get somewhere pretty. I am not necessarily referring to overbrowsed places like San Gimigniano, although it is very pretty. I guess I mean Cortona, Monteriggione, Sant'Angelo in Colle, Pienza, Montefollonico, Castellina. Castiglinone del Lago. But there are plenty more, maybe some closer to your big town choices.

Tim gave you excellent advice that I second. If you are using public transportation, that would be the deciding factor. If you have a car, Siena would be much easier to use as a home base.

If you could find good transportation from Siena to places you want to visit, I'd lean towards Siena since you'll be in Florence for three days. A quick look shows trains and buses from Siena to Lucca and Florence to Lucca. We stayed just outside Greve and took the commuter bus into Florence for a day trip. Riding the bus was fun, especially since we were the only tourists on the bus. Everyone else was going to work in the morning and returning in the evening.

Just want to confirm, yes dependent on trains/buses! And thank you for the small town suggestions.

I would head straight to Siena! We've spent a total of a week staying in Siena and would stay there again --- it's that great for art, architecture, and being walkable. The only person I know (same interests as yours and mine) who hated Siena went there as a day trip from Florence.

If you like Romanesque church exteriors, Lucca is a nice day trip from either Siena or Florence, although I would rather stay in Siena the whole time and see it thoroughly. So is Pistoia an easy day trip from either.

I would be torn between Modena and Arezzo as a day trip from Florence --- maybe Arezzo would win out if it also included Sansepolcro.

You've been to some wonderful places in Italy --- your list made me wonder if you have also been to Padua.

I haven't been to Padua! (But I think we might have talked about Genoa and the wonderful cemetery before I went?)

Rather than the list of where you've been before, give us the list of what you want visit this time, and it will be easier to suggest the best base.
If one wants to see Siena, the Chianti, the Val D'Orcia, Val D'Elsa, then a base in Siena makes sense, maybe more than Florence. But if you are interested in Lucca, Pistoia, Cortona, Emilia-Romagna, Arezzo, Cortona, Padua or others, then Florence makes better sense, logistically. Siena is not well served by trains, and is not served by high speed trains at all.

Ah, I'm a bit torn. Siena is my top priority... the train connection to Lucca isn't bad (and I do love trains).

Split your stay and visit Lucca from Florence.

If you’re visiting both Siena and Lucca both are more convenient from Florence by direct train (Siena by direct bus). This leaves an extra day for another day trip. Arezzo too is a convenient day trip from Florence by direct train.

I like to take the bus instead of the train when I’m going from Florence to Siena. The bus station is next to the main train station in Florence, and it is more convenient to be let off in Siena not far from the Campo.

I like the smaller cities, so I would probably choose to take the train to Lucca after arriving in Florence and stay there two nights. (Stay inside the circular wall.). Then spend the next two nights in Siena. But, staying in Florence gives you the option to be more flexible and go where you wish each day.

I like to take the bus instead of the train when I’m going from Florence to Siena.

Thanks Jean, that's what I meant to say and a direct train to Lucca.