I’m going to give you an advice that most SEO professionals disagree with, the opposite of what I’m going to tell you is repeated over and over again at beginners courses in SEO and they are all wrong.
A lot of SEO’s will tell you to keep your site structure as flat as possible, the fewer clicks to get to any page on the site the better. This usually results in navigations with hundreds of links pointing from every single page to a hundred other pages. The idea is that it will be easy for Google to index and you’ll flow plenty of PageRank to each page. This is a flawed idea.
First of all, Google does not index a site easier becasue of a bigger navigation. Our Head of SEO, Aaron Axelsson, could easily show even in 2012 that after removing the majority of the internal links on his own blog.
Pages in Googles index
The bump in indexed pages (apologies that the chart is in Swedish, it’s from Aarons Webmaster Tools) comes directly after Aaron removed more or less his whole navigation, now containing only 3 links, Home, Contact and About. The rest of the blog is just a number of posts on each page and pagination. Have a look at it, it’s interesting to see even if the language is impossible to understand.
Neither is it improving the positions for the site and the reason (that I can see) is the tax Google adds on links, there are diminishing returns on links. We’ve rebuilt a whole lot of sites in the way that we have removed large parts of the navigation, making the site deeper. This way we increase the relevance of the links that are actually there, instead of every single page on the site linking to the best goals in soccer only the pages in the soccer section do so. We’re also not throwing the PageRank around to anything but putting it where it’s needed. Yes, this is a form of PageRank Sculpting and no, we don’t use nofollow.
How do we do this?
It’s a rather straight forward strategy, remove any internal links that aren’t necessary and be as vigilant about it as you would be with external links on a site hit by the Penguin. Let the index page link only to the top categories, let the categories link to the products/articles in the categories and if there are too many products in a category consider subcategories instead. Make use of tags but stay clear of tag clouds and leave any site wide outbound links in the bin where they belong.