Circumventing structure is not a bad thing, doing things differently, telling a different narrative. Creating a new way to film, an experimental piece... But some of these things don't get their message across, and not because people are to stupid to get it, bu simply because the created missed the mark.
In the case of SGU specifically, they weren't reinventing the wheel. They weren't using a different storytelling technique that had never been used before. They were trying a very traditional, serialised narrative and they fell short in some of the requirements of that structure.