Color of numbers:
As you said the green color is used to make them stand out, you mostly remember what your skill does but there are many occasion you want to recheck some of the values, one of them often being skill damage comparison.
Due to mixed types of values we can't say that green is used to mark values that change which is usually the case.
Value of numbers:
Some of the values change by using runestones,but note that some skills completely change the way they work,so adding runestones actually changes the text along with the numbers.
Some values are constant during the whole game like some cooldowns,stun duration,mana costs,number of hits...
In D3 many skills use weapon damage percentage instead of actual skill damage to balance the game between melee and magic classes as they gather better and better equipment and progress levels.Because of the use of percentage on most skills there is not so many scalar values.
Some particular values are not in percentage and they have to scale with the player level to keep their usefulness on higher levels.Transcendence(monk) is one of those skills.Most likely these values are not in percentage to prevent their abuse and make them balanced in certain parts of the game depending on what point the blizzard thinks someone to be unbalanced...i still think they could be replaced by percentage in future.