In OoT, before the battle starts, he released a wave of dark energy that prevented Navi from helping, getting rid of Z-Targeting and the ability to read his weaknesses. Does that count as power nullification?
So since this seems to have transitioned into a general thread for Crenados abilities i think I'll share some of my recent thoughts. To start off with Ganon should have mind control as his alterego Jerry brainwashed hyrules soldiers.
A few of his abilities also stem from Twilight Magic, as far as I remember the only reason Ganon has soul manipulation is due to the twilight veil Zant used, and twilight magic also allows users to turn themselves into particles, create portals, and manipulate matter as Midna demonstrates here
Its implied they're the same person, unlike Yuga who was a entirety different person that just so happened to merge himself with Ganon. Here we see Ganons spirit rise from the body of Agahnim and then Ganons mentions how impressed he is that Link beat his alterego before the final battle begins.
I was actually meant to say he might have mind manipulation as opposed to he should have it, as some sources claim he had just possessed Agahnim, while others imply that they're the same person.