From Assisi to San Gimigniano

Perugia is a regional capital and yes, it's way bigger than Assisi. If it's worth a detour depends on what you want to see/do. Personally, I'd pick a different city, but since you're going from one small town to another, you might like seeing a bigger city, depending on how much time you have, and your patience looking for a parking space.

If you are looking for another small town to stop in for a few hours, how about Cortona?

If you want to shop for ceramics, Deruta is the main center, but Perugia and Assisi have some, too. I enjoyed Perugia for a couple of nights many years ago, mostly for atmosphere and the main-square sights, but it still hasn't made Rick's list of must-sees for a new visitor. (Perugia is the sister city of Seattle, which conveys instant importance.) There are escalators from several parking areas to the town, but I recall there still are some hills after that.

Thank you for all your replies. They've helped me a lot. We have been using Rick Steves guide and it has been more than helpful. We found it so useful and informative. I have another question. What are the most important towns in Tuscany we absolutley can't miss?