As far as I know, Indoctrination theory is more or less dead. At this point, I think most people just do what I do and ignore casey and mac's idiocy and substitute our own ending in.
Shepard killed all of Cerberus and stole the Normandy
-A from them. THE END.
Ha, just as valid as anything we got officially as far as I'm concerned. As for EA, they didn't smartly manage the game to start with, so I find it hard to take their side here.