The high level of customization and 'you can pretty much do anything you want' vibe of the whole application. For instance, the way in which any team's workflows can be directly translated to a block diagram is very powerful, and the scripting engine allows for some pretty deep add-on customization.
The robust API makes custom integrations easy for even an untrained programmer like myself.
The admin module (workflow editor, item details editor, etc.) is very easy to use and overall a great user experience. This is often overlooked in systems like these.
The concept behind workspaces and items and their relationships is easy to explain to just about any user, allowing them to cook up their own workspaces if they request them.
The entire document/attachment system. There's no bulk file imports, and everything is limited to a one-to-one item to file relationship. Large workarounds and scripts must be created to accommodate some very simple document management operations. Support has indicated that this is changing, but I've seen nothing in the last year.
The sourcing tab is very limited, and bulk import/export are not easy to accomplish (e.g. BOM scrubbing).
While attractive, the classification module is completely useless - the data cannot be exported, reported on, or displayed in BOMs.
Generally, although the scripting module powerful, it's clear that it's being used overused (out of the box) to write in features that ought to be easier to administrate (e.g. workflow approvals, custom part numbering)
It's also lacking out of the box integration with other Autodesk tools, even ones explicitly named Fusion!
BOM management, cross-team coordination, and rapid estimate generation for our entire prefab building system.
The ability to write a custom integration with Revit API has allowed us to automatically keep BOMs up to date on a project to project basis, with the simple click of a button.