Shepard is written with a Hesiod-ic. A Cassandra Syndrome, "the kid" is for-shadowing, to the inevitable conclusion. A Chekov's gun.
The Dream Sequences, are tropes from Gaius Baltar of BSG, complete with many other rip's of that franchise. Hall of the Dead, "It's in the Frakin Ship", Kera Thrace "Kara Remembers" so on and so forth. Gaius isn't convinced that he "ISN'T a cylon, until much later in the BSG story?.
When everything is revealed.
We never got the reveal. So we are left with a plot hole.
He is convinced that "God's Hand" is at work, as he frequently has visions of 6, just as Shep has visions of the God A.I. Gaius also IS an angel for the Cylon's 6 but this is never seen in the ME universe. So all we have is a 1 sided version.
Indoctrination, to me, is a vestigial tail, like dark energy, that was never fully realized in any meaningful or coherent way. Had it of been, we could of witnessed a trope of the Cassandra Syndrome, played in reverse, and had Shepard call BS on the "Hand of God" fate.
But that would be contrary to the "massive" retcon's of the universe given in ME3.
(It would of been sweet though) a true M. Night Shyamalan moment, but no, that is not what happens.
We could go with Philip K. Dick, and say "Total Recall", but that hurts more than helps in many respects. "If this is a dream, I don't want to wake up".
The catalyst, like the Trojan Horse, could be seen as the "final solution", but we have to know some Greek myth stories to really work that angle. Unfortunately, it ITSELF has to be "self-created", which in turn makes the case that it created the reapers.
Another plot hole. As no exposition is given as to WHY the catalyst exist in the first place, other than "it chooses to be".
That "it" had this plan all along, is plausible, if we simply accept that Shepard, is the chosen one, the Ubermensch a "Roy Batty vs. Tyrel", Lobster-Buddha, or Robo-Genetic-Jesus. This gets us into some "hard determinism" and "predestination" problems on both philosophical levels, and narrative levels. It happens when we play with Deus Ex Machina literary devices.
The cycle is no cycle, once the supreme organic comes to the rescue... again, a metaphysical problem, as the God A.I. never posits "why" organic life is important on any level.
What is so special about Shepard? Is he messianic or not?
We choose Ubermensch and "God" is dead. Cycle is broken. For a time? Who knows? -Roy Batty- Bladerunner- was Harrison Ford a replicant?
We choose Buddha, and we go to the void, with the reapers, as a reaper, and we escape Samsara. Samsara still exist, but WE get out. - Babylon 5 Sheridan Experience (this is rather contrary to Buddhist teachings though). Pop Culture version... go figure.
We choose Genetic Jesus, problem solved, diversity is ended, A.I. is no longer a threat, as it is no longer divergent from "God's Plan". - Battle Star Galactica - Hera
Legion helps us with this... but the "end game" writers, perhaps pressed for time, perhaps not as well versed as they could of been, ignore that explanation.
We just have to accept it. Just as Shepard, free from agency, has to accept "God's" explanation.
Alas, what we have is the Hesiod argument that even Zeus, cannot bend Fate for Achilles. Much as with any messianic archetype, Shep, has to kick the bucket. The "breath" plays off the Matrix - Neo ending, which in some ways could be seen as acknowledging the material, but taking it a different direction.
What is the God kid, other than Col. Sanders from the Matrix?
It struck me as last minute.
I would also add that we never fully see the destruction of the citadel, just the catalyst core.
I find the whole thing sloppy, poorly handled, poorly written... but that's my take.
There was (to me) a better narrative here... and it just slipped through the collective fingers of the writing staff.
Sorry... I guess?