First of all, upgrading stone quarry should not upgrade gold quarry, it makes things too easy to reach.
You could make visuals of buildinc changing when upgraded, add more buildings, add resources consumptions by peasans, upgrade individual houses so peasans become citisens and need more resources, add a craft system like in anno's game, well you can do so many things I can t list them all. Plan what kind of game you want to make and focus on the gameplay you think of ;) I m pretty sure you ll do it great :-D