I'm not an authority on the subject, but I'll offer this:
Plastic lenses can be quite clear when new. But their longevity may suffer for practical reasons.
1) Scratches. Glass is harder than plastic meaning it is less susceptible to scratches. Anybody who's ever worn glasses will know that the lenses smudge pretty easily, meaning that you'll have to clean the glasses frequently (sometimes, several times in a single day, depending). Usually this involves rubbing the lenses with a cloth or tissue. If the latter is chosen and the brand of tissue is microscopically abrasive you might inadvertently scratch the plastic lenses, although glass would be unscathed.
2) UV rays. Plastics can break down on the molecular level from the presence of ultraviolet light. Plastics contain long, complicated molecules in comparison to the very simple molecules of glass (both are amorphous in structure, but that doesn't really matter for this conversation). Compare the clear, plastic headlight enclosures of an old car, regularly parked in the sunlight, to those of a new car and you'll see what I mean there.
Of course, not all plastics are created equal. These are just some general thoughts.
In you original post you asked about the molecular properties. You can use chemistry to explain the molecular bonds. The chemical structure of glass is pretty much already at its lowest energy (and highest entropy) state -- there isn't a lower energy (or higher entropy) configuration that it is likely to break down to. Glass is quite stable in that respect. Clear plastics, in comparison, are nowhere near their lowest possible energy [thermodynamically speaking, on the chemical level.] As a off-shoot of this idea, if you heat up glass it just gets really hot (assuming you don't melt it*), and that's about it. If you heat up plastic it starts on fire**.
*[Edit: and even if you do melt it, it still turns back to solid glass when it cools]
**[I.e., It turns into something different, something that is decidedly not clear plastic.]