Gosh, where to start! Okay, the season. Yes, September, especially after the 15th when kids are back in school, is a perfect time to be in Italy. That is now our preferred time to be there. The heat is going away, the sea is still warm, and the tourist spots are getting quieter. Another poster mentioned staying in one place for a bit at a time. I agree, even though I love to drive. It is nice to settle in and really know a place. It is probably best to pick a region, or to really immerse into the larger cities. Also, don't be afraid to cross the border. If you are in Venice, it is really a shame not to visit the Veneto back country and Treviso, or even to get up to the Dolomites around Corvara in Badia and Cortina. Trieste also has it's charms, and the part of Croatia that is nearby (Istria) is beautiful. Slovenia too!!
It is also a shame not to use a car to get around. You have so much more access to the countryside and towns that way. The trick is to set things up so you avoid having the car in a major city, which is a hassle to be avoided. For example, you might rent a car from Marco Polo Airport in Venice, and drive around the region. You then renturn the car and take the vaporetto or the Alilaguna into Venice at the very end of your trip. Or you do it in reverse, or bookend with, say, Verona or Milan, returing the car to that city's airport. We frequently rent cars in Venice and then drop them off at Ciampino (Roma), spend a few days in Rome, then catch our plane stateside from Fiumicino (Leonardo Da Vinci).
Personally, we love Venice and its charms. It is much less crowded now that the cruise ships have been moved further away, and the neat thing about Venice is that it gets really quiet as soon as you walk 20mn in any direction away from St. Marks. The Giudecca, Arsenale, Lido, and Dorsoduro each have their charms and are all walkable 100%.
We also love most of Italy, but in particular the Lakes District (Como, Maggiore, etc), the Amalfi Coast, the Cinque Terre, and southern italy is amazing as well (Matera, Alborobello (Puglia), Lecce, Monopoli, the Gargano, etc.).
And then there is Sicily. Just beautiful. And perfect through October. The only issue with Sicily, is getting there this year, as I am not sure that Easyjet etc. have firm flight schedules. Major carriers into major cities may be OK, but I would expect the budget airlines to be chaotic for a while.
If you must take trains, allow lots of extra time for connections, as trains frequently do not run on time in Italy, and that was before Covid. It is not as bad as the UK, but it is not France or Germany. And be especially careful in stations, and even more so as 2 women travelling. You will get a lot of unwanted attention in these types of places, and you will be a target of pickpockets and Malvolenti.