I like the ideas of Endermen stealing away light. That way in a cave it would be hard to see anything other than their glowing eyes. How scary would it be if you wander into a dark corridor somewhere deep underground, but when you try to lay down a torch, nothing happens. You hear an ominous whispering that sounds like a distant echo,but you know the enemy is somewhere right beside you. You'd try to look around for the unseen enemy, but only looking with your peripheral vision.
Then when you accidentally stare it straight in the eye it would freeze. Everything would be silent but then when you take a step back he disappears with a menacing shriek. The whispering returns, but you can't see the enemy. You turn around to see him slowly approaching with his long slender arms reaching out. It's too late, he grabs you and holds you down. You constantly swing your sword trying to break free, but there is no time. Other creatures are closing in on you. You are surrounded and doomed.
Well there's my story explanation of what I think they should do. I also kinda think of them as creatures from the nether. I think requiring ender pearls to line your Hell Gates would be an interesting addition. But their name kinda implies that they come from the endlands rather than the nether.
Awsome Story very detailed.