The basics of pin mapping are simple and Eagle does it well. However this does not adequately address different needs that come up in the real world.
At least it's possible to not assign any pin to a pad.This takes care of situations where a part simply has physical pins that internally don't connect to anything.
Unfortunately the opposite is not possible. If I have a part that has either the one internal connection that can be physically accessed on multiple pins, I have to represent this in the symbol by multiple pins.