ME 3 SPOILERS! Mass effect IT

I don't buy into IT myself. There are some compelling arguments but I'm not sure they really add up. It could also be I just don't like the idea of Shepard being indoctrinated. There's no evidence to support the idea that a person can choose to accept or reject indoctrination. If Shepard is indoctrinated it's a done deal and s/he is just going to get worse over time. If that's the case, the Reapers won. No way around it.

Your points are in line with mine. It doesn't make sense to continue with hallucinations for someone dead or dying. Similarly, the story isn't really complete; or, rather, the galaxy fell to the Reapers once again unless we picked from the RGB choices. (Refusal is them winning.) The fact is, BioWare intended a trilogy. What we got was meant to be a complete story. Having Shepard indoctrinated means the story didn't really end.

I quite enjoy the IT and wouldn't have minded if that was the case and we had a sequel with a new character afterwards.

But yeah, it obviously wasn't what Bioware went with. The trilogy ended with the end of ME3.

Tali is also potentially around by the time Shepard boards the derelict Reaper, though not the Collector ship (which Garrus could be present for, I believe).  She's probably also eligible to be indoctrinated.

True, but they're never free.  I mean, I know sacrifice is a theme here, so a lot of people are okay with Shepard dying, but I want my Shepard to live happily ever after with his LI.  I suppose that's my love of post-Reaper War fanfic of which I've read tons.

The indoctrination theory is just a theory. It's only true if you prove it to be as such but you have to ask yourself what the ending is worth if the true canon is "Shepard got indoctrinated, saw a bunch of visions and nothing really happened after the climb to the Citadel and nobody knows whether the Reapers were beaten or not". Do you see? It makes it a non-resolution and there's not going to be a Mass Effect 4, so there is my answer: IT is a cleverly constructed lie woven with tangible proof but if you accept it as the real answer to the ambiguity of the ending you have no ending.

Not quite. It started out in March 2012 as a genuine theory. When BioWare announced that they would have more information on the ending at a PAX 2012 panel, some on the old BSN hoped that they would announce an indoctrination DLC, where the real ending to the game would be revealed. Of course, what they really announced then was the EC. The whole thing sounds like a quaint idea and fans letting their imagination run wild in retrospect but back then, we were still hoping for a miracle of sorts.

I was skeptical back in the day but I did love the idea of IT. If you look at the original ending, not the EC, there were a lot of things that fit the idea and not a lot of definitive counter arguments to it.
Sure, if BW had gone that route, they would have seriously pissed off anyone who didn't choose destroy but what I liked about the idea was this: It would have been a truly novel way to tell a story, and even more than that, it would have been storytelling that you can only achieve in an interactive medium like a video game, where the player/the audience needs to make a choice. BioWare, i.e. the reapers would have succeeded in actually indoctrinating not only Shepard (i.e. the player avatar in the game world) but a large number of the players themselves.
As I said, screwing with your audience in this way would have been a risky move but it would have been something that has never been done before and I think it might just have given some new impulses on what authors dare do in interactive media.

Alas, it wasn't supposed to be. IMO, the IT is thoroughly useless ever since BW announced that they were done with the ending and will never touch it again after the EC and Leviathan. Now, as you say, IT may be an interpretation but it doesn't really improve anything because even if you want to interpret the EC ending as Shepard being indoctrinated (which is hard to justify anyway IMO), where does it leave you? It would mean that Shepard never defeated the reapers, in fact, it would mean that we have no idea what happened after the beam run. Instead of a bad ending, you'd just get no ending at all. I don't think that's an improvement of the story.

So yea, the indoctrination theory was very cool IMO as long as it really was still a theory. Once that option was off the table, it unfortunately became useless in it's capacity to improve anything about the game.