Lets go back to season to in order to understand what was being built.
In the middle of the season you have a two part arch about Whan and how the first Avatar came to be.
When Wan finds his human and spirit friends fighting each other, he joins himself with Raava to pacify them; but this puts him in mortal danger, and can do nothing to stop the spirits from killing his friends. Upon traveling the Southern spirit portal with Raava, Wan battles Vaatu before convincing Raava to possess him.
Fighting Vaatu with the four elements, Harmonic Convergence occurs, causing the two portals to overlap with each other. Using the energy generated by the event, Wan fuses with Raava permanently, thereby becoming the first Avatar.
In the season finale after this huge build up of Unalaq trying to become a "dark avatar" for all intents and purposes he succeeds. We KNOW he succeeds due to the dark avatar state attacking republic city. For that brief period (before the completely illogical and inexplicable "Korra State" turns the tide of that fight)
Korra unlocks her innermost spiritual energy and teleports to Republic City to discover a fragment of Raava within Vaatu, for Vaatu cannot live without Raava. Jinora's spirit illuminates the fragment, and Korra withdraws Raava and purifies Unavaatu, destroying Unalaq.
Now put those two parts together. They fabricate the "origin" of the avatar so we know how the avatar came to be. Then push the story line foreshadowing the birth of a "dark Avatar" in Unalaq" who did in fact merge with Vaatu, much in the same way Wan originally merged with Raava. Unalaqs death in essence meant that a new "dark Avatar" cycle had to have been created, even if the first dark avatar was gimped and ham stringed at the starting gun. Moreover we know that there was a dark avatar and even though Vaatu was "vanquished" we understand that Vaatu can no more be destroyed than Raava can without completely upending the entire cosmos of this "universe"
Now with this potential new Dark Cycle there are ideas that reinforce it. We understand from the lore that light and dark are in opposition to each other and must be balanced. So if the light cycle was moving Earth, Fire, Air, Water, ....ect ect ect. Then the Dark cycle would have to revolve backwards. Given that Unalaq is the first Dark Avatar and his native element was water, then it stands to reason the dark cycle should run Water, Air, Fire, Earth.... Water, etc.
This notion is in fact reinforced and at the same time presents another element that should have been properly exploited. If Unalaq is the first Dark Avatar and his starting element was water, that means the next dark avatar would have to be a native airbender. Granted that was going to be pretty hard to envision an air bender being evil when you know all of the worlds airbenders and at the time it did not appear any more would be emerging soon. Oh wait, thats right... The one who effectively disrupted Unalaqs dark avatar state. Jinora.
Lets watch. (SEASON 2 Ending Spoiler Alert
During the battle, Jinora's spirit manifested in the form of light, and entered his body, pulling out a small, but usable, source of light from which Raava could reform. Korra's spirit subdued the Dark Avatar and ripped the light source out of his chest, recreating Raava. Korra's spirit subsequently performed the spirit purification ritual on Unalaq and Vaatu, vanquishing both of them.[3]
Now when Korra State sees that the tiny shard of Raava is free... Notice, Jinora is her own separated ball of yellow light... INSIDE the dark avatar state. More precisely her spirit has merged with that of Unalaq so as to wrest control of the dark state long enough to provide Korra with that opening to Raava.
Then Korra has to take Jinora's spirt and Raava back to the spirit world to end harmonic convergence. Jinora's spirit departs back to her corporeal form and Raava & Korra merge beginning their own rebooted Avatar cycle.
With Unalaq no where to be found (unless they pull a major resurrection out of their asses for the ending of season 4) So as far as anyone knows thus far for all intents the first Dark Avatar is dead. Now we understand light and darkness are two different things and truthfully light/Dark are different things than Good v Evil. We also saw "how" this Dark avatar was destroyed and that logically points to the transition between Dark Avatars to be different than how the avatar changes hands only upon the death of the former Avatar. In the case of the Dark Avatar, it is logical that the title has to be forcibly taken given the manner in which Jinora effectively consumed Unalaq in order to hold Vaatu in check long enough to free Raava. That means the dark avatar must be taken (or potentially given by, either forcibly or bequeathed) from the former dark avatar.
Now as for what should have happened predicated on this. First and foremost, Jinora would have to be heavily pushed to the forefront of season 3 in order to rapidly build up her character. In that process a major plot thread of the season would be
Jinoras story being plagued by intrusive visions of Unalaq goading her, pushing her moral compass, ect. Jinora trying to figure out why she is being tormented by Unalaq and what she could do to rid herself of his presence. As a misdirection Jinora misinterprets Unalaq as losing his corporeal form and now being left effectively as a spirit. However that assessment is wrong as what she is experiencing is the antithesis of Avatar Callback that Korra lost during season 2, and Unalaq is effectively the only historical dark avatar in that cycle that Jinora is accessible to.
Now from here, that would have left Season 3 as a throw away "exposition-ary" season. That would have been able to leave the whole "Zaheer" story arc mostly the same as it was. Zaheer could have been tied back into the Dark Avatar saga fairly easily, only with a few modifications. Effectively you would need to switch bending between Zaheer and his combustion bending girl friend leaving Zaheer some form of fire bender. The bulk of Season 3 could still have been the anti establishment trope they went with but instead have the climax with Zaheer coming to understand the only way to destroy the "authority" of the avatar was to become the voice of opposition against the current Avatar to undermine it. This presents the potential for the end of Season 3 being Zaheer dispensing with his "we need no rules" Anarchism and submit to the course of assuming the role of Dark Avatar. Which all this would set up a gut wrenching season 3 finale where Zaheer effectively kills Jinora to assume that role. With that tweak to his bending, it puts him as a native fire bender and would be logical in the path of the Dark Avatar Cycle.
So Recap.
Dark Avatar
Dark Avatar Cycle
Cycles run backwards from each other.
Dark avatar must be taken/given instead of randomly reincarnated like the Avatar.
Jinora is the Second Dark Avatar
Making Zaheer the Third dark avatar and not actually squandering Henry Rollins like what was done by season 3.
Season 4 built around Zaheer trying to forever render both Avatars powerless and pursue his "power to the people" goal he had from season 3 but lacked the means to do it without nullifying the avatars attempts to "balance" the world back to that status quo. Honestly to do anything else in my personal estimation is not only ham fisting the story, but its outright ignoring the story that was already being built.
