STRONG Advice for an Enterprise level repository is to separate item storage from diagram storage.
By all means place all the viewpoint diagrams in the TOGAF structure, but put ALL items in a separate branch - whose structure is NOT related to any methodology. There is NO methodologically based structure that will handle item storage to the satisfaction of all concerned.
In our case, because we use ArchiMate, as the basis (but vastly enhanced/modified)of our methodology/modelling, our items are in the Items branch, then separated by items aspect (Business/Application/Technology/Motivation/Implementation etc.) Then by type (for example: Business Objects, Business Processes, Business Functions etc.).
We have so many items that within each folder, we have a set of alphabetical folders (A,B,C etc.). Indeed for some types, we now have so many that we have gone to a second level of alpha: AA,AB, AC etc.
Our overnight processing harvests the items from wherever they have been placed (by the user or by EA) and puts them into the correct folder.
We also have separate branches for Enterprise level and Project level models. Each project gets its own Items folder and there is one Enterprise level folder.
YMMVWFU
Paolo