This is quite a busy itinerary! Just clarifying, you do already have your international flights in to Rome and out of Madrid, correct ? You'll want to take the train from Venice to Switzerland, so you would want to do Rome, Pisa, Venice, Switzerland, Paris, Madrid...if in fact your flights are confirmed. Going Rome-VCE-Pisa would be seriously backtracking. As far as hotel suggestions in each destination, it would depend on budget and requirements.