Taxonomy vs. Menu

I'm working on a site: http://www.articleinsider.com.

It looks like the person who originally set up the site chose to use article Taxonomy rather than Menus to organize the site, which contains 50,000+ articles.

Here are the issues for discussion:

1) What are the benefits of a taxonomy organization over a menu organization?

2) It seems that on some category level pages, there are articles (which rotate as you refresh the page) - while on other category level pages, there are simply links to articles or subcategory pages.

   a) Why do articles appear on some category level pages and not others?
   b) How can I get articles (non-rotating) to appear on all category level pages, thereby eliminating spammy-looking containing-almost-all-links type pages?

3) At the subcategory level, I also see the problem mentioned in #2, above. Additionally, when an article is added to a sub-category, it appears as a link in the main content area of the subcategory - YET, it is not a sub-sub-category to which additional articles can be added.

  a) How can I eliminate the spammy-looking containing-almost-all-links category and sub-category pages, display an article and yet still link to subcategories?
  b) How can I add sub-sub-categories to the site that don't also create spammy category pages?

4) Is it best to switch to a menu system to eliminate these category pages? Why or why not?

5) If switching is best, is there a programmatic way to do this (given that we have 50,000+ articles)?

Thank you for your feedback!
Lindsay