Refer https://forums.buildingsmart.org/t/what-would-you-like-to-see-most-in-the-modernization-of-ifc/
I suspect relationships were adopted due to the strong dependency on EXPRESS and STEP in design. Having a class serialized to STEP with lots of direct attributes isn’t ideal as every single attribute needs to be noted (even if null/empty).
I’d like to see many relationships made obsolete, although it might be that xml (or something similar) should be a dominant serialization format for this to happen.
Minimum I’d like to see the class they inherit from be changed from IfcRoot particularly so that Global Ids aren’t manufactured in many authoring applications.

It would make the implementation of the IFC Schema as an object database more straight forward.