Well, one piece I saw missing was mention of the synthesis option, I wonder if it matters much in discussing this topic or not.
Also, I figure providing the Codex entry for Indoctrination seems relevant here:
The Reapers: Indoctrination
Reaper "indoctrination" is an insidious means of corrupting organic minds, "reprogramming" the brain through physical and psychological conditioning using electromagnetic fields, infrasonic and ultrasonic noise, and other subliminal methods. The Reaper's resulting control over the limbic system leaves the victim highly susceptible to its suggestions.
Organics undergoing indoctrination may complain of headaches and buzzing or ringing in their ears. As time passes, they have feelings of "being watched" and hallucinations of "ghostly" presences. Ultimately, the Reaper gains the ability to use the victim's body to amplify its signals, manifesting as "alien" voices in the mind.
Indoctrination can create perfect deep cover agents. A Reaper's "suggestions" can manipulate victims into betraying friends, trusting enemies, or viewing the Reaper itself with superstitious awe. Should a Reaper subvert a well-placed political or military leader, the resulting chaos can bring down nations.
Long-term physical effects of the manipulation are unsustainable. Higher mental functioning decays, ultimately leaving the victim a gibbering animal. Rapid indoctrination is possible, but causes this decay in days or weeks. Slow, patient indoctrination allows the thrall to last for months or years.
So if the underlined is to be believed, there could have been an attempt to indoctrinate Shepard near the end, and certainly after the run to the Conduit.
The question is; where does it actually begin and end, if there really was an attempt? I've figured that it has to begin after getting hit by that energy beam, and maybe end only with that special scene of Shepard breathing in the rubble. But to be fair, it can be argued that it's not until Shepard loses consciousness again on the Citadel (before taking the Space Elevator) that Shepard could actively be getting indoctrinated that modifies how Shepard perceives the world, accepting what is being told by the Catalyst. The problem is interpreting what's being seen in the scene.
And the Breath scene could also mean anything at this point.
But, I also have a problem with how Shepard's gut wound is so similar to Anderson's wound in this section. But I dunno how to take it in one direction or another, without further details as to the nature of their injuries at this point.
And there are some problems I have with what the Catalyst says to Shepard, regarding it's relationship to the Reapers, but I'm too tired to parse my issues accurately. And I mean that, off-hand, I can't tell if it's 'Oh I'm superior to you, we are unknowable' stuff in talking to Shepard, or really just bad logic by the Catalyst.
And then the Normandy scene in FTL and that crash afterwards raises questions for me as well. But some of that falls into trying to interpret what's being presented, but also in what is known about how FTL travel is supposed to work in-universe.
Where the ship should not have been able to survive intact after snapping back to sub-light speeds after getting hit by that energy wave, and then getting exposed to radiation strong enough to engulf the ship in Cherenkov radiation, meaning that even seeing them step out of the Normandy they would really soon die from radiation sickness, anyway, was a problem.
So at any rate, one of the most common themes with looking at the ending is that too much is simply stated at us, without sufficient explanation; and I personally hoped for a brief synopsis of the fates of the Homeworlds, especially after that energy field tore through the Galaxy, changing the Galactic dynamic and likely sending everyone into a dark age.