I have encountered this question on every project I have been involved in. On one hand, having a locked down folder structure promotes standard navigation and storage. On the other hand, coming up with a folder structure template that everyone will understand and use is quite difficult.
On one project I was on, we convened a “governance committee” of about 10-15 people from the different business units to come up with a standard folder structure for the entire company. It took us about four 2 hr sessions to get to create a template structure. Each of the reps then presented the template to structure to his/her business unit. Let me say that, this was not the end of it. We had to have another 2-3 meetings to resolve naming schemes and whether we should add some additional sub-layers.
In the end, the governance committee agree that we would only impose structure at tier 1-3 levels. Anything below Tier 3, would be free form. A good software design usually requires input from all types of users and ultimately a solution will contain compromises between different group.