Currently the default navigation is the iPad navigation. I personally always use Navigation Tree. It would be great if this was tied to your user id, similarly to how the last Wave you've worked with is automatically selected. With it being stored in cookies, it gets cleared on a regular basis (and we are a non-persistent Citrix session to access DSP so it always get wiped out).
The plan is to completely redo the menu/tree navigation along with the new UI for DSP 7.0. There will no longer be 2 versions to of the menu to select from. The new navigation menu will utilize the best qualities of both versions and will be much more user friendly. If the plan happens to change, we will reconsider this request, but for now it will not be needed.