How to avoid duplicate categories

Question

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.

Answer 1

Just a side node:

In fashion stores where you have a lot of attributes I use a lot of filters instead of categories. Therefore I use this extension: http://www.manadev.com/seo-layered-navigation-plus (Demo, Doc, aso...) wich also has great SEO abilities.

While using this you end up with at best at a store where customers have all filters available all the time. So no matter where they are in the store they can filter what they want.

Hoep this is a little help.