These difficulties are not unique to CWE. For example, the problems of repeatability and mutual exclusiveness in vulnerability taxonomies has been well-documented since at least Ivan Krsul's PhD thesis [Krsul].
In the months leading to the release of CWE 1.0, we have been addressing this problem by:
building multiple different views within CWE, to support multiple audiences
improving the existing views so that their organization is more consistent