there is no pr gain on how you link but how you divide it will determine what gets more. if you link to all dirs from root then all would be same pr. if you link to one dir which links to another the pr goes down if one dir got more links into it than another dir. just depends on what you value more. one big page with stronger serp or more pages with the smaller dirs getting better serps than your big page.
minor comment. if i had one inbound from root to both the following url they would have same pr, regardless of directory length.