Looking back at it now after hearing what you said, Pig Ganon would have made more sense as a unique fighter in Melee than Ganondorf as he appeared in 5 games at that point while Ganondorf only appeared in 1 game at that time. I know they're technically the same character since Ganondorf was Ganon when he was human and before he turned into the pig demon. But turning Ganondorf into a clone/semi-clone of Captain Falcon not only screwed over Ganondorf's potential in the long run but it also possibly screwed over Pig Ganon ever getting a slot. This is one of the reasons why I want classic Pig Ganon in the roster so we can have a version of Ganon with a unique moveset. It's clear that the ship has sailed with Ganondorf and he is going to stay as a Captain Falcon semi-clone forever.
Did you forget that Melee had a strict deadline of 1 year?
Yes, 1 year! ONLY ONE!
It's no wonder Melee had so many clones.
Given how little time they had to actually make the game.
If they had more time, maybe we would've gotten more unique fighters.
But alas, this didn't come to pass.
And so Ganondorf being a clone of Captain Falcon, because their body types matched, was his only shot of getting in at the time.
The reason he was chosen over Ganon (other than "being too big" maybe) was simply because Ganondorf was a lot more popular at the time.
Of course he would be, with Ocarina of Time being the beloved game it was and still is today.
Besides, who decided that Ganon and Ganondorf are mutually exclusive and thus cannot co-exist in the same game?
Especially when we consider characters like Link (three Links), Zelda(Shiek) or Samus (Zero Suit Samus).
So yeah, this is nonsense.
All that's preventing Ganon from becoming a character is on Sakurai.
Either because he has no ideas for a moveset, because "he doesn't fit" or maybe even because Sakurai doesn't know about him.