One of my favorite SharePoint blogs - Paul Culmsee at CleverWorkarounds posted on some of the gotchas with Managed Metadata.
I originally found this when looking for how to use metadata in the Open dialog box of an Office 2010 application. In the mantra of metadata good/folders bad, the one hole was how Office Apps rendered large document libraries without folders in the open dialog box - not a good user experience. Metadata browsing in the dialog box would solve that. I consider this a partial solution.
These are important limitations to be aware of when designing solutions:
No matter what, the managed metadata store should be just that – managed.