When is it a good idea to build a permalink structure from scratch?

It’s a good idea when you don’t want to use the default structure 🙂

There are a lot (like really a lot..) of cases when site planning includes URL structure, it’s best to really have a grasp of this plan before you begin.

I would go as far as graphing out a representation of the relationships/slugs, that way you can compare it with the “default” structure to figure out if you can make an easy hack (hierarchy/hook) or you need something from scratch.

The http://codex.wordpress.org/Class_Reference/WP_Rewrite API is comprehesive and daunting at the same time.

I really recommend using CPT’s http://codex.wordpress.org/Function_Reference/register_post_type to create the custom structure instead of bending over the defualt posts/pages. It will make your life easier.