Prototypal vs Classical-Inheritance UnityScript

You can read about prototype-based program$$anonymous$$g here: http://en.wikipedia.org/wiki/Prototype-based_program$$anonymous$$g. A comparison with a class-based program$$anonymous$$g is also provided.

One of the key differences is that UnityScript (are you refering to C#?) has classes an javascript doesn't.

what about function.prototype stuff? really confusing

I don't use javascript in unity myself. Don't really know if it really supports prototypes as regular javascript does (javascript for browsers). Anyway, if your search is about the key differences between prototype/class based program$$anonymous$$g the wikipedia link should put you on your way :).