Well, it all boils down to having site-level parameters that can be overridden by instance level ones.
To achieve this I'd suggest to add a parameter setting on the package information in the APM. At the moment, the only actions are "edit" and "delete", but we could add a default value there.
Each package instance then would have these parameters as default values and they can be overridden manually. As a matter of fact, the default value will only work for new instances of the package, not for old ones (otherwise you get into trouble differentiating, if a change in the default value is actually what the current instance owner wants).
I'd not use site level parameters per se, as you should not decrease the number of control a (subsite) admin has over each instance of a package.
