That is such a fun ask, thank you so much for the prompt!!

I think it would depend on the target audience of that game (basically are we 2D Zelda-ing it or 3D Zelda-ing it), but I see a couple different options right off the bat:

Treasure-hunter who wants to steal various trinkets from different tribes, mostly for the thrill of the achievement, regardless of whether or not there's any justification (or consent) to this hoarding (and perhaps even putting the tribes at risk since their magical protections are gone?). This villain would do every dungeon before you (and perhaps leave an even bigger mess behind that you'd have to navigate) and gather every artifact before you can get your hands on them (maybe leaving only some kind of ghostly trail of their presence behind, so you can still use these objects but in a limited way, or on limited time, or by paying with a certain resource...) until finally setting their fancy on the Biggest Possible Artifact there is... and being granted Courage as a consequence/reward for their reckless yet selfish adventurous spirit. And then you fight this villain, and they have the exact same equipment as you. I think this villain could make for a neat little 2D Zelda guy! Challenging but not lore-breaking or anything too serious.

My mid-crazy level for a 3D Zelda villain would be: perhaps some kind of Zant-like figure, a sorcerer that had to face a terrifying entity and survived, but went insane and is now persuaded the world is too soft and wouldn't stand against the attack of the looming darkness trapped underneath the realm and planning to return, and so is devoted to plunging the kingdom into its personal hell as a preparation to face the Big Bad of the game, whoever that is, over-valuing Courage to the point of becoming cruel to softness and weakness and those who need protection (so basically making them through a living hell as a form of tough love). This villain would seek the Triforce as a means of defense against the perceived threat, not realizing perhaps the threat either: has been living inside of them all along and corrupting them from within, or that said threat was waiting in the shadows to seize the Triforce immediately after grooming that villain to do the work for them (wonder who that threat could be... nobody ever behaved that way in TLoZ canon before 😇). Perhaps that villain could be Sheikah, because that sort-of fits with their OoT characterization and that's cool and we could have dark!Sheikahs again and I'd be down for that a whole lot.

Okay final pitch, this one being the wildest by far: the spectre of an Ancient Hero, who would start the game with the Triforce of Courage already. Maybe this hero either fully vainquished Ganon or got trapped sealing that angry guy, and has been haunting Hyrule without clear purpose for eons. Maybe there's a new gerudo king, or maybe hylians start trying to become friends with a monster race that we used to oppose (maybe both!)... and a deep dark force begins opposing the effort, attacking everything deemed dangerous and impure. While this isn't nice and making things complicated, dangerous, and maybe needlessly traumatic, we would slowly cleanse different dungeons from fragments of that hero, hear of all the brutal things that hero went through and all the ways they shaped him, leaving him entirely lost and disconnected until he stopped being able to see nuance or think outside of the divine. Basically, the Hero's Shade becomes your antagonist, and you, as the new iteration of the hero, have to gently but firmly tell the Ancient Hero that his battles belong in the past, and it's now time to let go and stop clinging to his duty, and that you are more than capable of looking over the kingdom yourself. A kind of brutal passing of the torch between generations, with a brighter and more diverse and complicated future ahead (and perhaps we even squeeze in how the Ancient Hero refused to see Ganondorf's humanity in the last hour when he dealt the killing blow, and him haunting Hyrule is a result of Ganon's curse? just to squeeze in a complicated Ganon because of course <3)