I want to avoid having the same category several times. I'll start with an example to make things easier to explain. Let's take a store that sells, for example, sports goods (e.g. www.sportsshoes.com). You have a gender based root category (or two - mens/womens), but you also have gender as a subcategory of "running" or "shoes", etc. You also need to have a gender attribute, in case the user comes from a different category entirely (like choosing a brand), but still wants to filter by gender.
In the end you have one root category, one attribute and a couple of subcategories all for gender. Of course, it's the same for the other root categories. You end up with 80-90 different categories/attributes for what are essentially different combinations of 9-10 actual categories.
This solves the problem, but leads to a lot of duplicate content, which means:
- more work to create and maintain the catalog
- easier to make mistakes like listing a product in some, but not all of the correct categories
Note: While my background is web development, I'm fairly new to e-commerce in particular, so let me know if I'm making the wrong assumptions here or if my explanation is not clear.