I think the above suggestions are all good, but I'm doubtful about Bologna for you because of its size, though I very much enjoyed the city itself and used it as a base for day-trips in 2015. It really sounds as if you are looking for a place that is or at least feels smaller than Bologna. Of course, once you are settled in the historic district, you don't realize you're in such a large city.
If you place a premium on small, Vicenza might be better than Padua (though, again, I used the latter and liked it).
If you enjoy walks in the mountains (which can be quite flat), the Alto Adige/Sud Tirol is worth checking out. I'd consider Bolzano in addition to Bressanone even though Bolzano is quite a bit larger. The historic district in Bolzano is closer to the train station and bus stop, and Bolzano has several worthwhile museums. Both those cities have good bus service up into the Dolomites (with onward access by mountain lifts) as well as train service to neighboring towns and south to Verona. If you are planning a summer trip, be aware that many lodgings in this area do not have air conditioning, which you are quite likely to need, since both Bressanone and Bolzano are down in the valley, not at altitude. Assuming a willingness to hop on a bus to get higher up, this is a very good area to visit in high summer, since if a heat wave hits, the mountains are about the only place to get away from it.
One out-of-the-way possibility is Lecce in Puglia. It's a beautiful Baroque city, not terribly large but certainly larger than Orvieto. There's not a lot of train service down there, but in 2015 the tourist office was organizing van trips to surrounding small towns. The schedule depended on where visitors wanted to go and when, but it would work for someone spending a good bit of time in the area. The cost was 55 euros for a full day of being delivered to 4 or more small towns and dropped off near the key tourist points. One of the trips went as far as Matera in Basilicata. There are also public buses running out of Lecce, which would work when you were willing to go to just one (or possibly two) small towns per day. Puglia, however, positively bakes in the summer.