Granted, with too many options it could quickly get confusing (should this message go to stdout or stdinfo; is that message more informational or more debugging?), but I think that it could be managed.
Similarly, I think that Unix fell down by relying too much on unstructured text (in the sense that the structure isn't enforced, not in the sense that it's altogether absent): because of this, every single tool rolls its own format, and even very similar formats may have subtle incompatibilities.
I'd love to see a successor OS which builds on the lessons of Unix, Plan 9 and other conceptually brilliant OSes, but I fear the world will never see another successful operating system.