How many nights do you have in total?
Milan is worth a day. I would visit it on the day of arrival (if you land in the AM) or the day before your departure (if you fly out of Milan, since in that case you need to spend the night before your flight there).
I think both Orvieto and Assisi are worth a visit. And since they are so close to each other, you shouldn't eliminate either.
One full day each is plenty to see them. Of course, 2 nights in a place is really just one full day in that place (from dawn to night). So you could spend 2 nights in Assisi and 2 nights in Orvieto and have more than enough time to visit both.
Another alternative, if you have a car and only 3 nights available, is to stay 3 nights in one of the two locations and visit the other as a day trip. Orvieto and Assisi are less than 90 min drive apart. That would save you the pain of having to unpack/repack/check in & out from hotels twice, which probably takes longer than driving from one to the next. If you don't have a car the train trip is a bit longer than driving (2.5 hours on average, with one train change), still doable but a little less time available. It's up to you of course.