What to do when STL files aren't quite right

My latest article at Hackaday is all about When an STL File Isn't Quite Right and deals with some of the shortcomings of STL files, which are used to share 3D printable designs.

STL files aren't really a CAD format, they're not intended to be edited. This is troublesome when a file needs tweaking. The thing is that 3D CAD formats like STEP (which are non-proprietary) might be a good solution, but they're not even readable by most 3D printing applications. I wonder why this is?