So, the two things I listed,
another version of one of the two things I listed, the megaton punch I brought up in a previous post (yes, it causes shockwaves, but those are a result of the
megaton fist), "sealing magic" (why does this count but not Zelda's restraint magic?), and a "wave of darkness" that nullified
Navi (not Link's Triforce) that was more or less an exertion of battle aura.
I'd say outside from the fact he doesn't shoot the electric balls, Ganondorf's Melee moveset is a rather fitting set that incorporates the main aspects of that while serving it's purpose of copying C. Falcon's moveset.
So I will reiterate; Ganondorf's moves
at the time were not that drastic of a deviation of his character. But it's outdated now.
EDIT:
Edit: And although this came after Ocarina of Time, that damn sword they show him with couldn't have been used? At all?
He couldn't use the sword
and be a clone of Falcon, defeating the purpose of why he has the moves he had in the first place.
He was never intended to be in Melee; his addition came only when the clones were being added.