As former user of Gambit / ICEM, I miss a possibility to repair manually unwanted faces and edges, comparable to Gambit (merge faces manual to virtual faces). In some cases it can happen that the CAD-geometry is poor with small errors, which cannot be corrected. The usage of the automatic geometry repair can lead to extreme simple geometry repairs (faces will be deleted/ignored), not useful for further meshing options (mesh finer than cleaned-up geometries cannot be used, or divergence in simulation later on). By usage of manual merge possibilities you can simplifiy areas by your demand (I know that this is contraproductive to the philosphy of package). But sometimes, in Inventor you cannot clean up the geometries if required, so anywhere a " manual face/edge cleaner posibility" is necessary.
The basic design syntax from origin CAD should be kept, only in CFD some faces / areas will be collapsed to simplified parts, comparable to the mesher work flow.