Good idea. Maybe the dark link in my version can be something that ganon uses in hyrule field to try and kill you on your way to the finale? As in, you fight all the dark links on horseback and then do the big dark link finale right before you get to your destination/the giant mirror. It would be pretty cool.
He may have stolen the magic/technology to create the dopplegangers from Nihal.
I don't know. The whole final battle needs to feel relevant and not done before in a similar fashion. This is a totally different Hyrule, and Dark Link being in the Glass Chasm is more of a cameo than a big role. I can tell you right now that I'm not a fan of "darkside" characters in general, but he has been a part of the series since the second installment, so I owe respect to the character regardless of my feelings for his kind.
I'll explain my first idea of the final setup:
Link and The Errant discover the Ocarina of Time beneath the Hyrule City Ruins and use it to travel back 200 years to the day that Hyrule was invaded by the swarm of whatever insect species (we need to design them). They are amid the thriving Hyrule City, walking the streets when hundreds of windows from far above can be heard shattering. They look up to see countless insects propelling themselves into buildings, quickly devouring them. The two run for cover, through a building and out the other side. Together, they must fend off against a number of these insects (who again, aren't interested in killing people, but aren't pacifistic either). The Hyrule Army responds with loads of gunfire, effectively damaging a great number of buildings before the attack is called off by Queen Zelda (you hear a general shouting the order to his troops to flee the city). And so Hyrule has fallen. There's absolutely nothing the two heroes can do. They see a number of enormous insects (simply much larger brethren) join the feast, and so The Errant plays the Ocarina one last time to warp he and Link back to the current time, but they are separated: Link arrives in the proper time, but the Errant is sent back with the Ocarina to his time.
Link gathers himself in the same place beneath the Hyrule City ruins to only be greeted by none other than Ganondorf. They ensue battle amid a number of these insects, which eventually leads onto the backs of two of the larger species, and so the battle takes to the skies, soaring over the entire country. Link must shoot at Ganondorf with his bow, and use the hookshot to drag the other flying bug closer so he can lash at Ganondorf with his sword. Eventually, depending on whether or not Link or Ganondorf has delt more damage, one of the insects will tire and crash down in the Death Moutain Crater, plummeting through the remains of the Frozen Reactor (where it is unfortunately impaled, torn, and utterly destroyed by the scrap metal) and either Link or Ganondorf end up lying on a sheet of ice above the seemingly bottomless pit. The victor of that round will cinematically dive down to attack the downed opponent. At this point, you would have the ability to button-dodge the strike if you crashed. Otherwise, you'd have the ability to deal a great hit to Ganondorf. The final battle ensues, and ends when Ganondorf falls through the ice. The end; tired of typing.
Now that I've written that out, I don't know if I really like the idea, but it's better than scrapping it all and not releasing anything. Hope it'll serve as a source of inspiration, if nothing more.
EDIT: As for my username's origin and meaning... I'm not going to release that. I have you know that it's not borrowed or taken from anything else though.