Travel to Switzerland

My wife and I will be traveling independently to Europe for 5 weeks in April/May 2013. We want to focus on Switzerland but will be flying into and out of Berlin so will spend time in Berlin and Prague before arriving in Switzerland. We are looking for recommendations for 3 or 4 cities to stay in within Switzerland and want to see as much of the country as possible. We will be traveling by train and want to do as many of the panoramic train trips as possible including the Glacier Express and the Bernia Express. We would prefer to stay in apartments or B&Bs. Would appreciate any recommediatons that you have.