3D skeuomorphic interfaces were always good in theory. I think the problem with them is the keyboard. The mouse is capable of recording velocity (which is why it is used for aiming), whereas the keyboard is binary. This distinction is crucially important for navigating quickly through interfaces. If I want to switch apps or tabs, I can typically do it with a very quick flick of my mouse. In 3D I would have to walk over to my new task which could take a significant amount of time depending on how far away it is from me.
Nobody wants to explore a 100 story virtual mall when they can just type in exactly what they are looking for. It could maybe work for Ikea, but the markets where this could work are so incredibly niche.
The advantage that computers bring is that they don't have to work like the real world. I am sure that our current approach to VR interfaces (which is 3d skeuomorphic) is a dead-end; there exists a more productive method that works nothing like our reality.
Regardless, the 2D browser was the better approach. Cool does not equate to usable.