There are three solutions to this quest:
Use one master account/pricebook, and rely on the whole single store permission behavior/permissions to give each store access to what they need.
2. Use seperate accounts for each store, and ask for support to give you access to company hopper allowing you to switch between accounts/companies where each store is completely separate
3. A sort of hybrid solution, is to create "price groups" by making one account for every price group. Example: Say you have 100 stores, 2 in every state. You have 50 accounts. Each account manages a region/state/etc. (i.e. a group) and you can have "only" 50 different pricebooks instead of 100.