First of there is need for getting the shared cart function to work, as it's a expected multistore feature, and probably should be considered a bug when it's not available.

Though ... this idea is more about adding more support for deciding what should be available for each store. Including but not restricted to currencies, languages, payments, shippings, coupons, vouchers etc.

T.ex. when you edit a language, there should be a multi select for stores on it, as store owners often would like to restrict this per store.

Example, this and other multistore extensions from the same dev:
http://www.opencart.com/index.php?route=extension/extension/info&extension_id=26035

But it could also be a one screen, listing all currencies, shipping, payments etc per store with check-boxes (a bit like the user permission screens).