Any ending that is "all in the person's mind", to any form of story telling, whether it's a novel, movie, or videogame, is just a cop-out. With the exception to the ending to Inception of course since the entire plot of that movie revolves around the mind, so it makes sense in the context. But to pull a fast one on the reader at the very last 1% of the narrative is just a lazy way for writers to address plot-holes in their stories without having to resort to actual work to fix their stories.
I think that if the Indoctrination Ending was the actual goal of BioWare, their most grievous error was making it too subtle, too hard for people to figure out. And the "all in one's mind" being a cop out - you're referring to entire movies where the entire length of the movie was actually just in the main character's mind. The slow play mind fuck. I don't see any problem with having 99% of the content of this game being real, and a small 1% of the game being an actual real mind trip. Hell, we're dealing with a game where ME1's main enemy Saren was under mind control (that was the whole point), ME2's main plot was centered around using mind control and the Illusive Man is in the early stages of mind control, and ME3's plot has the Illusive Man and his minions now completely 100% under mind control. Did you expect something different? You can argue that ME is just like Inception since so much of it revolves around the mind, just with far more additional complexity in the plot.
I was reading all these posts blasting the ending for being this and that, the only thing different was the color of the explosions, etc. So I was prepared for a complete let down when I played the ending for myself.
It was anything but.
1. I immediately noticed some weirdness during the ending portion. After I got hit by the laser I was sad seeing Liara and Garrus laying in pools of their own blood. I was confused at the infinite ammo pistol that took normal enemies down with no problem. I figured that they just had to do this because at this point the coders can't really put out enemies at full strength and expect the player to fend them off limping with just a pistol and no shields.
2. I remember being very confused that the radio said no one survived and that they were all pulling out. Hello? I survived... *waves*
3. I get transported to the hall of dead bodies and hear Anderson. WTF.... the radio said no one survived.
4. I tried shooting the collector with my pistol and nothing.
5. I limp to Anderson, do the whole cut scene thing with Illusive Man, shoot Anderson, shoot Illusive Man, sit down with Anderson and feeling very confused when Shepard is nursing a bleeding wound in his side. When did that happen? I figured it was just from the initial laser charge thing.
6. I see the boy ghost thing and thought WTF is the boy doing here? And I had also figured that Shepard's nightmares of the boy in the woods didn't really mean anything. They were just used to create artistic whatevers, to show that he was stressing and thinking of the boy.
7. Then I destroy everything and I get the heartbeat ending and by this time I was really confused. Why am I now buried in rubble... on Earth?
8. I was far more confused at the ending than being let down by the simplicity of it, hence the reason I searched for an explanation for it. I went in prepared for a really simple, rushed ending with one of 3 colors. I instead got something that left me with more questions because the ending just didn't make sense.
To me the Indoctrination ending fills in all the holes that I had during my own playthrough.