I did the tour in 2014 and stayed extra nights ahead in Venice but WISH I had stayed at least one extra night in Padua. I found so much to do there that I didn't get to. I didn't mind the Al Fagiano either - traveled with brother and SIL and they didn't mind either. I just hate to do one-nighters so I almost always stay in the tour hotel the night or 2 before. I loved the Scrovegni Chapel frescoes. If I were to do this trip again, I ~might~ book myself in to the Scrovegni before the tour as well just so I could have 2 passes at it. You are only allowed to stay in there for 15 minutes after you have been in the antechamber for 15 minutes. There is SO much to see in there and really, I am not a big fresco fan!
At the end of the trip, I'm afraid I'm one that didn't find much to do in Orta San Giulio. We did stay an extra night and wished we had spent the morning there doing the Sacra Monte, then headed in to Milan after lunch. It WAS raining heavily when we were there, plus it was the middle of Oct and things were closing up. Excellent gelato at Gelato Artiginale Eliot on the main piazza of Orta San Giulio. Your guide will start working on exit strategies by about day 3 and will group people in taxis and shuttles if you wish. We took a shuttle in to Milan with 2 other tour members, so there were 5 of us and it worked out really well (again because it was pouring rain!).
I would spend the 2 nights in Milan but I know others don't find much there. Two nights just gives you 1 full day. Check on the closing day for The Last Supper fresco by Leonardo da Vinci if you want to see that. Seems like the closure day was why we did not see it on our afternoon in Milan.
Another thing I tried to do on this trip was see all the relics. That might sound ghoulish but really, lots of chapels/cathedrals/basilicas with remains of saints. Start with the Basilica of Saint Anthony in Padua for his jawbone, tongue and vocal cords and move on from there.
I agree with the others that this is a FUN trip! Do work to be in as good a physical shape as you can be. I had just come off some other tours so was good to go as far as walking up and down hills but I noted on several Trip Reports this year people have commented on the strenuous walking.