Perhaps a Greater Vault could be put on an extra level at the end of the reverse-levels section of the CoC. You know, where you jump down 5 levels or so, and then go up instead of down? At the end of that sequence, when you reach the level with only two down staircases, I'd add an up staircase that leads to a level with a guaranteed greater vault. I would restrict the possibilities in that greater vault, to make sure that its contents aren't overpowered. Think of it as a Greater equivalent of the vault on PC:6.
I'd then add another Greater Vault, guaranteed to be a real challenge, in some sort of "end game" location, a location that you can't even access until you reach a certain level, or complete some difficult task. Make it so that it's filled with one of the hardest types of beings to handle, and you've got a real challenge on your hands.