Hardy Ferentschik and I discussed a few issues on IRC today:

Regarding ReflectHelper#getFieldTypes

(11:53:47 AM) hardy__: 1. you are only inspecting declared fields, but you really would also need to check getters
(11:54:34 AM) hardy__: 2. Also your handling of the TypeVariable is wrong (just no code which runs into it)
(11:55:22 AM) hardy__: 3. You don't handle ParameterizedType at all, which is the primary failure for EmbeddedGenericsTest
(11:57:04 AM) hardy__: in terms of TypeVariable and ParameterizedType, we really need to fully resolve the type using classmate
(11:57:17 AM) hardy__: see AnnotationBindingContextImpl in this context
(11:58:19 AM) hardy__: the TypeResolver in AnnotationBindingContextImpl is really a singleton and could be moved into some until class (for example ReflectHelper)

Hardy added something like the following to handle the ParameterizedType, but it may not be complete:

if ( type instanceof ParameterizedType ) {
    fieldTypes.add( (Class<?>) ( (ParameterizedType) type ).getRawType() );
}

This goes back to the original question. Do we want to leave this auto-discovery code in, or rip it out (enforcing that @Embeddables be explicitly listed in the annotated classes)? I'd argue that Steve Ebersole's point may be the best solution: fix the implementation, but disable it by default, hiding it behind a new setting(s).

For now, it's fairly low-hanging fruit. We might want to just disable it now and update all unit tests to correctly list all annotated classes.