I personally prefer grouping classes logically then within that include a subpackage for each functional participation.
Goals of packaging
Packages are after all about grouping things together - the idea being related classes live close to each other. If they live in the same package they can take advantage of package private to limit visibility. The problem is lumping all your view and persitance stuff into one package can lead to a lot of classes being mixed up into a single package. The next sensible thing to do is thus create view, persistance, util sub packages and refactor classes accordingly. Underfortunately protected and package private scoping does not support the concept of the current package and sub package as this would aide in enforcing such visibility rules.
I see now value in separation via functionality becase what value is there to group all the view related stuff. Things in this naming strategy become disconnected with some classes in the view whilst others are in persistance and so on.
An example of my logical packaging structure
For purposes of illustration lets name two modules - ill use the name module as a concept that groups classes under a particular branch of a pacckage tree.
apple.model
apple.store
banana.model
banana.store
Advantages
A client using the Banana.store.BananaStore is only exposed to the functionality we wish to make available. The hibernate version is an implementation detail which they do not need to be aware nor should they see these classes as they add clutter to storage operations.
Other Logical v Functional advantages
The further up towards the root the broader the scope becomes and things belonging to one package start to exhibit more and more dependencies on things belonging to toher modules. If one were to examine for example the "banana" module most of the dependencies would be limited to within that module. In fact most helpers under "banana" would not be referenced at all outside this package scope.
Why functionality ?
What value does one achieve by lumping things based on functionality. Most classes in such a case are independent of each other with little or no need to take advantage of package private methods or classes. Refactoring them so into their own subpackages gains little but does help reduce the clutter.
Developer changes to the system
When developers are tasked to make changes that are a bit more than trivial it seems silly that potentially they have changes that include files from all areas of the package tree. With the logical structured approach their changes are more local within the same part of the package tree which just seems right.