My question is with regards to the best multisite setup in terms of link juice/reputation strategy.
Is it better to set up as subdomain (www.site1.mainiste.com) or subdirectories (www.mainsite/site1.com)?
The reason I'm asking is that subdomains get indexed by search engines as "separate individual websites" as opposed to subdirectories which are seen as an extension of the "main website".
For example if I were to create a multisite network of 100 food related sites as subdomains with each site having a "related foods directory" page with links to each other. These links would have keyword rich anchors with keyword rich descriptions as well.
So that would mean in the above example that each site would have 99 sites linking in. Because they are subdomains would search engines then see the links as reputation building because they are coming from "separate, individual" domains. In essence the sites would be "recommending" each other.
The number of subdomain sites could grow to a few hundred just as an example and therefore create in theory more lining "recommendations" to each other.
As opposed to subdirectories where the links may be considered "internal" links instead and not as valuable in terms of reputation building? Or does this subdirectory strategy work as well as far as reputation building interlinking is concerned?
This this thing would be a new site/with subdomains, so the main site would not already have any link juice. In this scenario which would be the best strategy, subdomain or subdirectory or are they equal?