Hello,
I currently use Inventor 2013. The biggest trouble I have with any project is managing files. I've just started using Vault and although things are better, when the project gets huge, managing the project tree is still a nightmare. From main Assembly- Subassembly- Parts- IDW/DWG- DWF- PDF- Quotes/Invoices can be an absolute mess of files and folders. Even when it is organised into nice categories, navigating the project that has thousands of files is not an easy task.
Proposition: The navigation bar is great for just the assembly. An extension to it could be made where file names can be changed, comments added, and that links the parts to their detail drawings and CAD drawings or Excel calc files. The navigation bar extension should be a mind map of every file in the project. Branches of the project tree could be minimised depending on the detail you want seen. Files could be dragged to the bar and would automatically snap to the closest file and then be linked to that file. It would remove the tedious task of keeping track of part numbers and file names as you could just follow the branch of the project tree.