Ideally, a good design involved both science and art. Good craftsmanship combined both components into a beautiful product that did the job in the most elegant fashion possible.
Their cubular-shaped shuttle design was anything but elegant. It was as blunt as a brick and flew like one.
That didn't matter much in space because the vacuum environment didn't care for concepts such as aerodynamics.
However, once the shuttle plunged into a terrestrial planet with a breathable atmosphere, this ugly cube shape became an absolute detriment to the shuttle's airworthiness.