Okay, here's the problem with Indoctrination theory:
So, Shepard "beats" indoctrination with Destroy. Then he wakes up on Earth.
On Earth.
Half-dead. No one got to the Citadel, no one opened it up, no one connected the Crucible to whatever the "real" Catalyst is, no one destroyed the Reapers.
Shepard "defeats" the Reapers in his mind, but not in reality.
So... how is that a "better" ending?
I have my own "indoctrination theory". Casey Hudson was "indoctrinated" by the 'ol peace pipe after coming off a binge of reading Singularity literature, and then wrote the ending.
Don't get me wrong, the implications of the Catalyst actually being that "Star Child/Master Reaper AI/Part of the Citadel" nonsense blows pretty much everything plot-wise into hell.
My ending is that everything up to Anderson dying is the end. The Citadel opens, the Crucible connects, then BOOM! cut to Destroy ending.