9 day Itinerary Help

Is that actually nine nights in Italy? Three nights in one location is only two full days. A few more days would be ideal. (See the itinerary of the RS tour as an example, and that tour has all the transportation arranged.)
I'd start in Venice and end in Rome. It's easier flying into Venice, than out of it. Also, Venice is better to walk off jet lag and acclimate to Italy. Rome is big and bustling. Work up to it.
Review the Trip Reports on Italy and read the posts under the Italy section to get suggestions.
Have a great time planning.

Your itinerary is probably the most popular plan to see Italy. So much so that Venezia, Firenze and Roma now are called “The Holy Trinity” of Italian destinations.
All three are beautiful and fascinating with layers of history in each city.
Then again, if you’re already in Florence, you’re so close to charming places like Siena, Lucca, Pisa, Santa Margherita Ligure and Camogli along with the Cinque Terre’s 5 famous towns. I could easily spend two weeks there.
From Venice high-speed trains reach Florence in 2:15. From Florence, Rome is 90 minutes away by high-speed train. There are two train companies with high-speed trains traveling from Venice to Florence and Florence to Rome. The least expensive Trenitalia train tickets go on sale online 6 months (180 days) in advance of the train’s departure date. You can buy the tickets NOW online on the websites of Trenitalia (www.trenitalia.it). or The Trainline (www.TheTrainline.com) which shows the Venice to Florence least expensive train ticket at $19-$26 during mid-May. At that price the ticket is nonrefundable and unchangeable so be sure of your dates before buying your tickets. The Florence to Rome tickets start at $22 on Trenitalia’s high-speed Frecciarosa trains.
For a quick look at timetables and ticket prices, I check the Trainline’s website which will also list trains of all the train companies such as Italotreno. ( www.Italotreno.it ) and Trenitalia. Trenitalia’s English website is www.trenitalia.com/en

My first trip to Italy was to the three big cities of the Holy Trinity. With the attractions mostly condensed into the citiies’ historic centers, and with so many other travelers concentrating on visiting mostly the same attractions, the daily lines and crowds can wear thin.
So, be sure to schedule time to do what the Italians discovered in living each day to the fullest: “Dolce far Niente” — the sweetness of doing nothing.

Do you have the RS Italy book? We used it for our first trip and found it invaluable.

Thanks for the responses.
Did a little bit of research and came up with a new plan of skipping Venice for this trip. Instead spend time in Rome, Florence, Siena and the surrounding towns.
Also am thinking of renting a car after 3 days in Rome and then driving to Florence. Car may provide more flexibility in exploring Tuscany and will also be cheaper when you consider train tickets for 3 passengers. Parking could be an issue though?
Any advice on this?

I prefer your updated plan. The car in Tuscany will be a huge plus. This spring I was in Tuscany traveling by train / bus and was hamstrung by it. The car will give you lots of options. But I would go to Siena from Rome for 2 nights and then on to Florence. Siena is between Rome and Florence.

I would plan a day trip to roam Tuscany with car. Pick up car at airport and drop off there when returning to Florence. Unlike most airports, the Fliorence airport is close to town and an easy,not expensive taxi ride to town. I think there is also public transportation to town, but we use a taxi.

I think skipping Venice this time is wise. We did the big 3 on our first trip, but we had 18 days!
Look carefully into the cost of parking, when reconsidering a car rental. Normally, a car is useful when touring Tuscany; however, with the amount of time you have, you may be able to construct an itinerary, including only towns accessible by public transport.

The car will be useless on the days you're seeing Florence's sights, and you can get to Siena from Florence by bus in less than 90 minutes and not need to worry about parking a car. I bet it would be cheaper just to rent the car in Florence for the day(s) you plan to visit rural Tuscany.

Rome to Florence travel time:

By car 2 hr. 56 min. (estimate from ViaMichelin.com, could take longer)
By train maximum of 1 hr. 37 min. for the Freccia trains.

If you are confident about your travel date, you can buy those train tickets way, way ahead of time for as little as 14.90 euros per person. You can see that fare for random January trains on trenitalia.com.

The competing train company, Italo, advertises some tickets on that route as low as 9.90 euros.

If you are staying in the Tuscan countryside a car is almost essential. I’d explore Autoeurope.com to see if any companies do a one way rental Rome to Florence. But if you’re not planning to spend a few nights in Turscany, the train would definitely be better. The ride is usually 2-3 hours.

Thanks for all the replies!
Another reason for leaning towards car rental is that we have 3 suitcases and 3 backpacks to carry. I know that its too much but its unavoidable due to various reasons. Are there any luggage restrictions on trains and buses?

The only restriction on luggage is your ability to get it on and off the train/bus. Also, be very careful about leaving luggage in an unattended rental car.

The car will be useless on the days you're seeing Florence's sights,
and you can get to Siena from Florence by bus in less than 90 minutes
and not need to worry about parking a car. I bet it would be cheaper
just to rent the car in Florence for the day(s) you plan to visit
rural Tuscany.

Ditto this. You definitely do not want the hassle of a car in Florence, and be aware that you cannot drive into the historic centers of most Tuscan towns, such as Siena's. Read up on ZTLs if you haven't yet? :O)

...be very careful about leaving luggage in an unattended rental car

Ditto this too. I wouldn't personally want to leave anything at all that I couldn't afford to lose in an unattended vehicle.

As ponygirl813 said, there are no luggage restrictions for the trains/buses. Your larger bags will be stowed in a compartment under longer-distance or airport coach-type buses. For trains, depending on bag size and carriage arrangement, they'll fit in a rack above your head, between the seats (don't place them ON the seats) or in dedicated baggage areas at the front or back of the carriage. The trains are great; with some exceptions you can get on in the middle of one city and off smack in the middle of another, and all 3 of you can watch the scenery instead of the road. Siena is one of those exceptions: the train station is below the city; buses do have drop-offs in the upper city.