Contrary to popular belief, clones were added in Melee because they had extra time; they probably could have added two characters with unique movesets, but they chose six "cloned" characters to fill out the roster.
As I recall, Ganondorf was planned to have a sword-based moveset, but that idea was ditched early on. But when they decided to add clones, they went back to Ganondorf's model and noticed that he had similar proportions to Captain Falcon, and realized that they could make him a slower, stronger clone of the Cap. So they did, but as anyone with an AR can tell you, they kept the sword in the code (and for one of his victories).
Just a bit of backstory for those of you who were wondering.
For Brawl, Ganondorf will very likely have his own moveset - again, the only reason he was a clone of Captain Falcon was because creating a unique moveset for him would take too much dev time. But Brawl had much more dev time than Melee, hence greater chances of Ganondorf having a sword. for his moves.
If Sakurai does want to keep Ganondorf's Melee moveset around, there's two ways to do it: Blood Falcon (a literal biological clone of Captain Falcon) or Black Shadow (Falcon's archenemy). Both would make sense with a slower, stronger Falcon moveset, and they could Luigify it by adding in some of 64 Falcon's moves and diversifying the specials a bit. I've thought about this at great length, and I've come up for a decent moveset for a Luigified Falcon clone.
A: Melee Ganondorf (single quick punch)
Ftilt: Melee Ganondorf (kick)
Dash: I think it's the same in both
Fsmash: 64 Falcon (burning kick, would probably be shadowy instead)
Dtilt: Same in both
Dsmash: 64 Falcon
Utilt: Melee Ganondorf (laggy but powerful overhead kick)
Usmash: 64 Falcon
Nair: Melee Ganondorf
Fair: Melee Ganondorf
Dair: Melee Ganondorf
Bair, Uair: Same in both
Neutral B: Shadow Punch - Charges up energy in both hands (same amount of time as Warlock Punch). First punches with right hand, which does 10% damage with little knockback and somewhat shorter range, but high hitstun. Then hits with the second punch, which deals 24% damage and has the same knockback as Warlock Punch.
Side B: Shadow Boost - Same as Gerudo Dragon (I think it was called), but it can be directed in any direction. Has a bit more lag before the attack, allowing players to move in the desired direction, and a bit faster and more distance.
Down B: Shadow Dive - No, it's not a typo. On the ground, they lunge forward some distance with a lot of lag afterwards. If they're in the air and above another character, they dive down towards that character. Either way, they grab the character and launch them in the direction the user is facing. Only does 10% damage and low knockback, but can be used repeatedly.
Up B: Shadow Kick - Same thing as the Falcon Kick, but propels them upwards diagonally (on both ground and the air). Since it's now an Up B, it puts them in helpless state afterwards.
Final Smash: I dunno. Probably a "dark" version of whatever Falcon's is.
