Maybe the issue that is that we cannot work out the theory, the equations that correctly describe it all properly. Maybe dark energy and dark matter and not actually 'other stuff' but just an indication that there are errors in our theories. Fix the theory and the 'other stuff' disappears. Quantum physics and General Relativity need to be combined at some point and doing so may resolve everything! Or it could simply be that human intelligence is not capable of finding the solution. In the same way a dog is never going to understand calculus, maybe you need an IQ of 1,000 or 10,000 to solve physics.