Would there be some particular structure that everyone would agree on?
Alternatively, what is the desired structure you want?
Because the current format is so messy, I just focus on what I believe is most important: titles and externallinks. IMO, often the most interesting content in an article is lifted from content found via the external links. I also would like to capture the talk pages. Maybe just the contributing usernames and IP addresses.
Opinions or explanations that have no supporting reference are inexpensive. One can always these for free on the web. No problem recruiting "contributors" for that sort of "content".
Back to the question: I am curious what structure would you envision would be best for Wikipedia data? Assume hypothetically that a "perfect" parser has been written for you to do the transformation.