I guess I don't buy this - there are systems which offer a lot of freedom and are still popular.
Legos, Jeeps, Cooking. HTML, Minecraft, some real-world, software options.
"Usability" can be something you buy on top of the simple system, or it can be free, depending. These aren't diametrically opposite properties of systems.
Linux based OSes will never be popular and have the same freedom they have. The principles the developers have that make it free are the same ones that create these "usability problems" which make it so unpopular.