Perhaps Nighthawksh is thinking of places a bit larger than we are assuming. Some examples might help us provide more specific information.
I spend a lot of time visiting smaller cities, though few that I would term "villages". Even when train service exists, there are times when buses are more convenient due to direct routing, frequency, or the location of the bus stop vs. the train station. They may also be cheaper.
If there is a cluster of small places to be visited in a condensed area, more than you would be able to see conveniently on a single day via public transportation (3 is usually really pushing it), it's worth Googling to see whether there might be one-day bus tours that hit a lot of places on your list. I do that very rarely, but it can be worth it as an occasional splurge. I lucked out by finding some extremely affordable van trips radiating out of Lecce in Puglia last year. They were about 55 euros per person, transportation only.
Another possibility, if one of you can drive a manual-transmission car, would be to rent cars selectively for 1, 2 or 3 days at a time when the geography makes a car especially helpful, such as for the Tuscan or Umbrian hill towns. For covering small rural areas, gas, toll, and parking costs should be pretty minimal.
For all the reasons alluded to, I suspect that you will spend less time on trains than you anticipate. My gut feeling is that a rail pass will not save you money, but only sketching out your trip and adding up the 2nd-class rail fares will allow you to decide. Just don't rush to buy a rail pass. Folks here can give you good guidance on that decision after you have a possible itinerary.
Rome2Rio.com will help you estimate the travel time between stops and will identify where there is bus and train service, though you'll have to follow a lot of links to see the frequency of service. That would be my first step (after reading guidebooks), to see what might be possible. Then I'd get into more precise train schedules and costs at the French and Italian rail web sites. Trenitalia requires you to use the Italian spellings for cities.
You didn't mention what time of year you plan to take your trip. One thing to keep in mind when you're hitting a lot of smaller places by public transportation is your exposure to the weather. There will necessarily be a good bit of time spent hanging around small-town bus stops (typically outdoors, may or may not be covered) and non-air-conditioned railroad stations. Small towns typically have pretty infrequent service, and the penalty for cutting it too close may be 3 or 4 hours of cooling your heels in a little town you've already seen. They tyranny of the schedule is the price you pay for visiting a spot that--with luck--isn't very touristy.
Time of year may also affect how comfortable you are with sort of winging it--making your hotel reservations only a day or two or three in advance. That's the way I travel, but it's not for everyone, and it means you can't pin down your hotel costs before departure. Of course, you'd be nuts not to reserve in advance for your first night and last night.