OK, I’ve done another Mortis rewatch (in reverse this time), and I think something’s coming together. It kind of works as a vision of the future of the battle for Anakin’s soul and how dark/light/balance swing as he acts. It also shows Obi-Wan’s failure to control Anakin’s darkness, and Ahsoka’s success in eluding his poisonous influence.

I think the main metaphor-story works as follows:

This is a place of tests. Temptation is close here. Light, dark, and balance are personified.
Various wanderings and cryptic visions. Qui-Gon is involved.
Noble Obi-Wan, beginning to follow Qui-Gon’s more balanced footsteps, is granted a dream dagger, perhaps representing his role as master and fulcrum of their fates.
Ahsoka’s vision tells her that Anakin’s darkness will poison her to the dark as well unless she leaves him - but then in this world she becomes that vision of her dark potential self (like Luke in Vader’s helmet in the Dagobah cave).
Anakin faces Ahsoka. She’s displaying all of her worse impulses and resentments. They fight. Obi-Wan joins, but does not use his dagger to save her, representing his failiure to train Anakin (and thus Ahsoka) above their worse impulses.
Their conflict empowers the metaphor-beings, who fight until Father throws them into the same arena as our characters. (This is the only time we’ll see them appear to have real agency, but I want it to feel like a reaction to what our characters are doing, not independent of it.)
The dark leaves Ahsoka, but also kills her. (Good enough metaphor for her upcoming fall.)
Obi-Wan hesitates to use his dream-dagger to kill the Son. He fails to defeat the darkness. (Works nicely with his future character arc.)
Darkness tries to kill balance, but light tries to save balance, and dies in the process. (It’s not about defeating what we hate, it’s about saving what we love, plus ironically darkness has made things imbalanced anyway. This also works as a metaphor for Anakin’s turn, how he tries to grow in both dark and light under Palpatine, but kills his light instead, becoming Vader.)
Anakin takes the last of Daughter’s life force to save Ahsoka. He finishes off the light because of his connection to another. (Good enough metaphor.)
With Daughter (light) now dead, Son (dark) is now more powerful.
Balance tries to entreat Anakin to recognise his role in all of this.
To defeat darkness, balance kills itself. Anakin then kils darkness (as he eventually will at the end of his journey).
Dream ends.

Beyond those mentioned in my previous post, I think we should (and can) drop a few subplots:

We don’t need the test where Father makes Anakin choose Obi-Wan or Ahsoka, to which he forces both the lightside and darkside to bow to him. Firstly it’s too on the nose, secondly it’s not how his temptation plays out, and thirdly it muddles the Chosen One prophecy by implying that the father wants him to stay and embody the literal balance from Mortis. The better moment here is the conclusion of the second episode, where Anakin can’t let Ahsoka go, and takes the last life from the light side to preserve her. That’s a better metaphor for how his arc plays out.
We don’t need the visions of the future at all, actually. They don’t really go anywhere. He gets the vision of his future, accepts the darkside in order to avoid that future, threatens Obi-Wan, goes to threaten Ahsoka but she eludes him and rescues Obi-Wan, nearly lets the Son escape, but then the Son disappears and the Father removes that memory. We’re back where we started, with the only real value for the viewer being ‘Anakin’s been tempted by the darkside, and it looks like he’ll do bad things in future’, which this episode’s already doing all over the place. But the temptation here also isn’t how his future arc plays out. Plus it contains a LOT of un-dreamlike mundane travel, and removing this and the above means we actually have no ship or speeder bikes. I could MAYBE put this content in, near the end, but I think it’d be better without.
We don’t need Son trying to kill Father, since Father doesn’t appear weak until he’s actually fatally stabbed later. All we should preserve of their story is them as metaphors.

Instead, I think we could play it out as follows:

In the crawl, find some reason to get them there that includes Qui-Gon’s guidance (and use more Qui-Gon VO throughout).
Using a scene from episode 2, in a dream (its VFX are more dreamlike), Anakin sees himself, and then the Son emerges from the other himself, and threatens him. (This is a good first scene, since it implies the Son is more closely related to the darkness within Anakin, than a character in his own right.)
Anakin wakes with a start on the ship. Cut that into the original start of the first episode, but remove the diamond, just have white light wash over the ship.
The party wake up on the planet. Trim a lot of dialogue to not have them question the mundane stuff (like the ship) too much, keep them focused on the weird. They walk outside.
At the point where Anakin originally reacts to Daughter’s voice (but Obi-Wan and Ahsoka don’t hear it), use Qui-Gon’s voice instead - “He is the chosen one”. THEN, when Daughter appears, it’s with her asking “Is he the one?” We’re now implying some link between Qui-Gon and what’s going on here.
Have Daughter guide them down the cliff path until they get separated. Daughter walks off, leaving Anakin walking alone, and Obi-Wan and Ahsoka together.
Obi-Wan and Ahsoka find their ship gone, and then Son appears and taunts them. (Now, because of the inclusion of the original dream scene, he’s taunted all three. The darkside is present here.) He flies away, and they seek shelter.
Using a scene from episode 3, Anakin (alone) encounters Qui-Gon, who gives him cryptic guidance. Now Qui-Gon is clearly involved.
Anakin makes it to Father’s monastery. I’ll steal one of his lines from ep3 to replace part of his explanation of what he is: “I am an old fool who believed he could control the future.” No idea what that means, but it’s weird in a good way. They talk about Anakin’s destiny, which is one of the few threads I can do something with. Anakin is invited to stay for the night.
In a cave, Qui-Gon appears to Obi-Wan. They talk about Anakin. This is all clearly about Anakin, rather than the others.
Ahsoka receives a vision of her future self warning that there’s darkness in Anakin that will corrupt her if she stays with him - I could use THIS as all the explanation we need for why she’s darkside later??
Anakin wakes in the temple and encouters Shmi, where he talks about his guilt. She’s not explicitly the Son, it’s left mysterious. We DON’T then have Anakin threaten the Father, because that dialogue is all way too explicit.
In the morning, Ahsoka and Obi-Wan go wandering and talk about more weirdness, then Obi-Wan is grabbed by Daughter, and Ahsoka is grabbed by Son. I’ll use this to skip over the end of episode one and into episode two. Now we don’t need to have Ahsoka captured as they try to escape, nor Obi-Wan guided by Daughter again.
I COULD keep Ahsoka being bitten by the Son to explain why she goes dark here, but I think leaving it based on her earlier vision might be better as it’d be less explicitly because of the Son being a real person.
Daughter takes Obi-Wan to the dagger. I’ll probably add more Qui-Gon voice here.
Anakin scales a tower (I don’t think I’ll bother explaining why he’s there), and finds dark Ahsoka there.
NOTE: I COULD precede the previous scene with the one of Qui-Gon guiding Anakin, because he also has lines about ‘it’s very darkside up ahead’ (originally referencing the fire pit where Anakin has the vision). But I think it’s better off early?
Anakin and Ahsoka fight. Obi-Wan shows up and joins the fight. He considers using the dagger to free Ahsoka.
With less dialogue, so it’s implied they’re reacting to the chaos around them, Daughter and Son come into conflict. I’ll only show this briefly, before Father forces them into the arena where the others are fighting.
Ahsoka takes the dagger and hands it to Son, who kills her with a tap to the forehead. (The darkside doesn’t need Ahsoka, just power, or whatever.) Anakin is angry but can’t hurt the Son.
Son tries to kill Father, Daughter intervenes and gets stabbed. Son flees in remorse (fine).
The planet goes unbalanced, but Anakin uses dying Daughter to save Ahsoka. Minor wrap-up to these scenes? Might just fade to white.
The three plus Father appear in the monastery of balance. (Father even says “I have brought you here…” to help with this weird transition.)
I might extend the above scene by just cutting snippets out of other interesting things the Father says to Anakin throughout the episodes, ignoring geography altogether. Might as well get weird with it if I can make it seem like it has a point.
Son appears, and they all attack him. Father takes the dagger and uses it to kill himself. (Something something balance).
But Anakin uses the distraction to properly kill Son. (This works as a metaphor for the very future of Anakin. The dark was the last to fall, as Vader turns to the light to destroy Palpatine, but until The Force Awakens again, the power of light, dark, and balance, is now quieted.)
In his final words, Father says cryptic stuff about Anakin. The planet shatters and stuff.
In a flash, the trio awaken on the ship in space, and mysteriously reconnect with Rex.

I think this is a thing, guys!