The reason one does not see freely rotating bodies such as wheels or propellers in nature comes down to perhaps the most fundamental aspect of biological systems: they're alive. Because they're alive, resources need to be supplied to them and waste needs to be removed. Propagating nutrients across a freely rotating interface can be an intractable problem, and this is not even considering the question of _how_ one could induce free and unbounded rotation in a biological joint. Think of how muscles work, with discrete attachment points and it becomes clear that free rotation isn't possible with muscles. The only method of inducing rotation I can come up with off the top of my head is some sort of turbine design, with rotation being driven by fluid flow.
The notable exception to the absence of free rotation in nature is the flagellum, which solves the nutrient supply issue by being so small and self-contained that it doesn't need nutrients, just the presence of an ion concentration gradient.