And that's all
Other than that, his moveset wasn't so faithful to his series (And so was his playstyle). Seriously, WIZARD'S KICK? WARLOCK PUNCH?
But it wasn't unrealistic to the character at all. Keep in mind that Ganondorf uses the Triforce of POWER. Powerful moves make sense. His moveset was mostly based around strength, something he's well known for. While I was annoyed he was still a clone in Brawl, there could've been way worse choices.
For example, let's say they added MegaMan, making him a near identical version of Samus. What's the difference here? They share nothing but a regular blaster in common.
Now, at first, you might say Falcon and Ganondorf don't share anything in common. But they do. They're both muscle warriors with extreme strength. Likewise, Wizard's Foot and Warlock Punch were clearly powered by magic itself. So he indeed did incorporate magic into his moveset, just not the traditional way of projectile spells. Buffs are magic too, after all.
Don't get me wrong, I would've rather he not be a clone, but it wasn't as bad as people are making it. Plus, he was a pretty decent character in Melee anyway. Mid Tier isn't too bad for a clone.
Keep in mind I'm not defending the idea of clones, I'm just saying that people are complaining too much on this one. Lucas having almost the exact special moves as Ness bothered me more than any other ones, honestly.
As for Paper Mario, he has more than enough moves to not be a clone, but I won't lie: If he were in, the chances of him being a clone since he IS Mario is fairly high.