I actually love the IT for most of the reasons you seem to dislike it.

I don't really mind what happens after Shepard resists (or doesn't resist) indoctrination, in fact I kind of prefer it that way, not all stories need a happy ending and a lot of the reason I still love Mass Effect is because of the IT. For me it added an entirely new level to something I already absolutely loved. Being able to play through the entire trilogy again with the IT in mind made it a totally different game. I was thinking about this game with blue aliens and dumb space magic everyday for months and I fucking loved it, I still love it.

As for the choices at the end I can totally see where you are coming from in terms of game design and traditional story writing. I obviously think the ending could have been done better, but the entire game has you fighting a war whilst reminding you that you will probably not win. Your friends die, races get wiped out, their planets get destroyed and all you can do is look for something that can get you out of this mess which you aren't even sure will work anyway (The Crucible & the help of the other races). Having a choice doesn't necessarily mean everything goes exactly like you wanted it to.

As far as plot holes are concerned, at least the IT addressed more than the extended cut did. And someone has "resisted" Indoctrination before, Saren manages to resist on Virmire for a short amount of time before giving in once more, and so does Matriarch Benezia, this was pulled straight from the wiki on Indoctrination.

The mental damage from indoctrination is severe and permanent. As Shepard saw, the captured salarians on Virmire had been turned into shambling husks, who either attacked on sight or just stood awaiting orders. Only people with immense mental strength are able to resist indoctrination, and even then, only for a short time. Matriarch Benezia used her abilities to keep a 'haven' in her mind free of indoctrination, hoping for a chance to use it, but this meant she was effectively trapped in her own mind, watching in horror as she committed atrocities on Saren's orders. When mortally injured on Noveria, a despairing Benezia refused Shepard's offer of help and chose to die, saying "I am not myself, I never will be again."

Why doesn't Harbinger just blast Shepard instead of trying to indoctrinate him? Well, he did, the only time you see Shepard even survive the blast is when you pick the high EMS destroy ending, and even then you only see him/her take one breath. Harbinger doesn't go into "Indoctrination mode" or anything like that, Shepard almost dies and is now in the most mentally weak state he/she has been in during the entire trilogy, it makes sense that the first time the usually headstrong Shepard really starts to give into indoctrination (Fourth if you count the Dream sequences, which is an entirely different topic all together) is after watching their friends die and nearly being killed after doing literally everything he/she can do to stop the Reapers. I also hear people say that if Shepard is indoctrinated then why doesn't the Prothean VI on Thessia detect his Indoctrination but then detect Kai leng's right after? That's because the entire point of the IT is about whether or not Shepard gives into indoctrination during the end of ME3 or not, depending on your choice of choosing the the high EMS destroy ending or not.

There's also the topic of symbolism in the final scene. Such as Shepard being forced by the Illusive man to shoot Anderson, then the camera panning down to show that Shepard is now bleeding from the exact place where Anderson was shot immediately after Anderson dies. The three IT documentaries go into this much more but a lot of it can definitely seen as grasping at straws. And sorry for linking 4 hours of video.

I LOVE the IT, the fact that I'm even bothering to type this fucking novel-length comment at 4 am that I'm probably just going to delete tomorrow anyway is a testament to that, but I can absolutely see why people could hate it and just see it as a stupid fan theory. Either way, everybody is on this subreddit because they love this series, and that's all that really matters.

Sincerely - Someone who should really go to fucking bed