At the moment, categories are pushed right to the bottom of the page. This is mostly useful, but not always; it causes policy issues if there are stub templates around. While this is not something we can or will support, the fact remains that we're essentially imposing a structure on wikis by saying "categories will always go at the bottom".
What would be a nice way around this problem, at least with existing articles, is to have newly-added categories stuck immediately after existing categories - wherever they are in the page. We get some degree of consistency within articles that would otherwise be lacking.