Uh, no. Every version of Link is a composite character design who uses the most iconic of moves. Young Link can't do the Downthrust or Upthrust either. It's clearly not just a pure representation of one game or another.
Other than being his most defining trait and literally the most important part of the character called Ganon(who is the same person as Ganondorf), being the wielder of Triforce of Power, you mean?
Ganondorf did not use a Sword or Trident in OOT, the first game. If that's the only one to go off of? No, he would have no weapon. It'd be irrelevant. He also has never used a Trident in any canon game. That's explicitly Moblin Ganon's weapon. HW is irrelevant in that. Hell, Moblin Ganon used Swords first. This isn't even counting the fact that Ganondorf is still using magic here. It's just physical magic. Something that is an actual thing. The lack of a projectile is jarring, agreed, but by the time it could've been implemented in Brawl, tons of Zelda characters already used it, even ones not remotely related to Ganon or Ganondorf in someway. It became just a really interesting move to use, not a signature move for Ganondorf. Ganondorf actually lacks any real signature moves.
Funky and Dark Samus aren't in the same boat. Funky does not share any remote potential animations and has a very different body frame and style. Ganondorf does not look awkward with Falcon's animations in comparison. It still fits his actual character really well. Dark Samus could be that, but we've seen the character in Smash already using different moves. Ganondorf also has shown the compete capability to do the things he does in Smash. None of it comes off as weird for him to channel his triforce and magic into more physical attacks. Again, there is no questioning his trait is POWER. It's who he is. If he isn't showing that off, it's really inaccurate to him. He's a power character through and through in the Zelda series. Unofficial games aside.
So then he wouldn't be in the game at all otherwise. Still fits him as he doesn't actually have different abilities than Pit whatsoever. And he still separates himself in Smash by using different weapons(bar the Orbitars). So he's acting extremely accurate. The issue is that he's not interesting to play as because you can't formulate a new strategy with him, unlike the other clones. It has nothing to do with the fact he's actually severely accurate to Uprising.