Time required in a town depends on your interests. First, are there museums you want to go to? Second, how many churches will you visit for more than a few minutes? Many important churches have audio guides you can rent. In my experience, using an audio guide substantially increases the amount of time I spend at a sight. Third, how much time do you think you'll want for just wandering around the historic district, absorbing the atmosphere? This can be one hour for a quick overview or it can by much, much longer if you're like me and try to walk every street in the centro storico.
Which of the places you listed are absolute musts? I'm guessing those would be Venice and Florence.
How many nights will you have in Europe? The number of really usable days is one less than the number of nights, because that first day will be jetlagged. So do you have 13 truly usable days, 14 or 15?
Pisa is a quick partial-day side-trip from Florence. San Marino is geographically inconvenient, and I'd suggest skipping it on this trip.
Genoa, Milan and Turin are rather large cities that will take some time to navigate irrespective of how many sights you plan to see. You can probably get more sightseeing done in one day in smaller cities like Verona and Padua. Milan and (especially) Turin are sort of out of the way even if you manage to include the Cinque Terre. Of course, Milan might turn out to be a good city to fly home from.
Since you enjoy smaller cities, I want to mention a place that is geographically convenient, given other points of interest to you: Vicenza has a small-town feel within its historic district and is located between Padua and Verona.
And many travelers who visit Florence spend a day or two making side-trips to some of the surrounding small towns. That would add to the time needed in Florence, of course.
Finally, just in case Milan makes it into your final itinerary: Bergamo is a rather short train ride from Milan and is a charming hill town, especially recommended if you don't have time for any of the Tuscan hill towns while you're in Florence.
Edited to add:
I should have mentioned that many travelers squeeze Pisa and Lucca into one day-trip out of Florence. Lucca (town with walkable wall, not as tourist-clogged as Pisa) needs substantially more time than Pisa, and one clever poster here suggested going to Lucca first and hitting Pisa in mid-afternoon, as the bus tours are beginning to depart. That sounds better that tackling Pisa at mid-morning along with the throngs.