Ganondorf can use the Twilight Realm, the Dark World, and the gap between dimensions for pretty much whatever he wants, with the latter being used primarily for BFR. I doubt that will really bother Shinnok too much, but I don't think Sub-Zero can do anything about it.
Ganondorf can also become invisible and intangible, and is a able to set things on fire from very far away. He can seal people in crystals and teleport them, as well as paralyze them for a short time. He's also shown mind control and possession.
What does Shinnok's amulet do, and can he take a castle and/or island breaking attack with it? Or any of the other stuff?