What is PLY?

The Stanford format, built for scanned data. Its distinguishing feature is per-vertex attributes: colour, normals, confidence values, whatever the scanner recorded. Research and photogrammetry tools default to it for exactly that reason.

What is STL?

The language of 3D printing. It describes a surface as a heap of triangles and nothing else - no colour, no texture, no structure - which is exactly as much as a slicer needs. There's an ASCII flavour and a binary one about a fifth the size.