Make Tabs-on-Top an option per Notebook, because the best UI is dependent on the user's data.
Tabs on top works best with a small number of categories (6-7 max). For example, a student may have one notebook per semester, with one tab per course. Because a student won't be enrolled in more than 6 or 7 courses, tabs are the best option because they allow quick switching between courses during the day.
A vertical list is probably better for projects with a large number of categories (more than 6-7), or where categories are often added. For example, a business notebook organized around clients and projects. If the business is acquiring new clients, then the number of categories may grow past 6-7 fairly quickly. In such a use case, quickly switching between clients may be less important than having them all in one notebook.
In other words, the best user interface is dependent on the user's data and how she wants to work. Because Microsoft can't control what the users will do with OneNote, they can't present the best interface using one standard layout. Therefore, Microsoft should make Tabs-on-Top an option, per Notebook, to allow the user to select the best option for his particular use case.