User blog comment:Kaloneous/Mass Effect 3 Ending DLC Denied and PAX/@comment-4945364-20120405200733/@comment-4950455-20120406025953

But none of that's actually in the game, so it's still just essentially making up your own ending, the same as anyone who just completely disregards the entire post-Conduit sequence.

In other words, as an attempt to explain the various plot holes of the ending while staying entirely in-universe, the indoctrination theory is satisfactory though flawed. But as an actual ending, it's either woefully incomplete or no different from any other of the "fix" fanfictions that are undoubtedly springing up around the internet. So I don't see the special appeal.