Too bad you weren't going into Malpensa. I could give you some tips on where to stay. But I do know that there is a youth hostel in Milan. Plus the hotels near the train station are "very" cheap. It seems to be a safe part of town but there is a lot of graffiti about giving you an unsettling feeling.
Thanks for the tip on Brussels. I am going to have to consider that sometime. But I am going to Italy again this year. It was my first tour ever last year. I had a great time but it did not go as smoothly as I wanted. There are better options as far as airfare such as Ireland and the Netherlands but somehow I feel the need to go back to Italy and try again, to do it right.
Pavia is just south of Milan and is a great little town. It has a large castle and there is also the Certosa di Pavia nearby. I know of a great little B&B there. Let me know if interested. But if you and your wife are in decent shape then consider the lake region.
Here are some things I learned on my trip.
Try to settle on one or two regions and then a few provinces within that region. The Touring Club Italiano maps are great but the regional maps just don't have enough detail. Try to get you hands on the provincial maps. They are free at each province's tourist information office. The TCI maps can also be purchased here
You can determine what town a province is in here
Avoid the need to be in a different place every night. Italy should be savored. There are lots of wonderful little towns in which to stay. Find a place you like ans stay a couple of days. Keep the place as a base for day rides.
Finding a place to stay can be a little stressful. If you don't speak Italian and are in a non tourist area, getting directions can be difficult. This is another good reason to not jump around too much.
Remember that there are other places in Italy to see other than the tourist areas. We were somewhat of a novelty when we rolled into town on our bicycles. People always had lots of questions. any times only in Italian! I speak very little Italian but I seemed to somehow be able to answer at least some of their questions.
Try to avoid the large cities. They can be very busy and not very bike friendly. There are plenty of small towns near by where you can stay. You can leave the bikes at your base and take a train into the city.
At some time you may need to get to a city to catch a train. Many trains do not allow bikes that are unboxed or not in a bag. Most regionale trains allow bicycles. They really should consider relaxing the rules for bicycles IMHO.
Look for the markets. Most towns of a decent size will have one. They are usually open around 9 or 10 and this is a great place to get some lunch.
Here are some other links: