I have been researching custom publish types from Morten Rand-Hendriksen's great tutorial on creating a WordPress portfolio theme on lynda.com. He demos how to setup a custom taxonomy for "quality recipes" and make links like domain.com/?quality recipes=publish-title. I believe this is actually awesome because you receive a publish-title using the contextual clue of "quality recipes" without having to be tied to a lot of nested hierarchical subdirectory archives that might be boring to check out and contain repetitious content.
For any large, multifaceted domain, It could be neat if there's a method to create a site work as it features a permalink structure such as this: domain.com/%publish_type%/%postname%/ for posts and custom publish types, while remaining with domain.com/page-reputation for pages.
I am considering domain.com/blog/publish-reputation for anything within the blog, though domain.com/?blog=publish-title would still work.
What is your opinion, and what's the most practical method to carry out this?