My husband and I just did a very similar itinerary:
Venice 3 nights train to
Florence 3 nights
Rental car 6 nights- 2 in Siena, 2 in Montepulciano, 2 in Assisi, dropped car Spoleto then train to
Rome- 5 nights.
If I could do it over I would have stayed in Florence for 4 nights and done Siena as a day trip. It was so difficult getting into Siena- you will not need or want a car there at all- we intended to take a day drive on our 2nd day there but it had been such a hassle getting parked and into our hotel we opted to just stay put. While we liked Siena- the Duomo is fabulous- we didn't like it as much as we thought we would and regretted 2 nights there. For a “pedestrian only” center it is incredibly busy with car traffic!
That said- since the Chianti and Tuscany areas you want to see are all so close- all can easily be reached as day trips and you can combine several hill towns in one day- an hour to here, 45 min to there, etc- I would suggest basing yourselves for 3 nights somewhere central- perhaps an agriturismo or an easier to access hill town. We loved Montepulciano and Pienza.
Those one night stays take a lot of time/effort- I would aim for at least 2 night stays when possible, 3 is even better. I would suggest this:
Venice 3 nights
Florence 4 nights with day trip to Siena
Pick up rental car
Tuscany Hill Town- 3 nights
Orvieto- drop car then stay 1 night
Train to Rome 4 nights
Or you could go from Florence to Siena via bus or train, stay 1 night then pick up your rental car in Siena.
The drive from Florence to Siena along Chianti Road was fine but so short- not sure that area really needs a full night.
We stayed at the beautiful Palazzo Carletti in Montepulciano, has dedicated parking spots just outside the wall- a very short walk from there to the hotel. Super easy to come and go. We hated to leave and wished we had stayed there all 4 Tuscany nights!
Other hotels- I did post reviews for some of these:
Venice- Hotel Ala
Florence- Hotel Calzaiuoli
Siena- Palazzo Ravizza- see my posted review
Montepulciano- Palazzo Carletti
Rome- Albergo Cesari
All were great for location, bkft, comfort, etc. I would stay at any again except the Palazzo Ravizza in Siena.