1. Do not spend too much in Geneva. Can consider going to Bern or Lucern.
2. Do not spend too much in Milan. Nothing to watch now. Duomo is under reconstruction. Book your ticket to watch Last Supper now.
3. Half day in Pisa is enough. (1 hr to Fizenze by train)
4. Must go to Siena, as 1984 said.
5. Spend at least 3 days in Roma. So many things to see.
