We were trying to use iRhino 'in anger' for the first time a couple of days ago. One immediate issue cropped up which was that we had multiple design options within one rhino file, organised in a hierarchy of layers. Unfortunately, iRhino does not appear to handle nested layers so it was almost impossible to figure out which layers were which.
The fairly simple work around was to save out each option as a separate file, but this would not work if the hierarchy was needed for a reason other than options.
For general file organisation, being able to work with nested layers would be a fantastic improvement.