Jumping in from consoles, since there's more active discussion here.
I am in the minority willing to live with the current endings. Maybe the lack of closure will be settled in future lore via more games, DLC or literature. Sure, I'd have changed some things if wrote the story...but I can say the same about a number of movies and books I still love. Even so, while destroying the relays and all synthetics may be suboptimal, it doesn't disallow for a continuation of the ME universe. (Besides, I always intended for my Shepard to sacrifice himself if the option came up; and the Geth all died and EDI was in my vaporized party for my 1st playthrough anyway).
I'd definitely like to believe this indoctrination theory is a possibility. It's interesting and would make me feel like I got played...in a good way. It really would be pretty brilliant. Hell, even if it wasn't their original plan, BW should co-opt it.
One hopes that if further ending DLC is released, that there some more consequences as result of choices included. Like, for example, during another push battle, biotic artillery help with reduced effectiveness for all waves as support roles, or greatly help the final waves as front line troops, but perish in the process. An entire krogan battalion engaging a reaper for tactical distraction and glory. Perhaps they succeed under Wrex and fail under Wreave. Stuff like that...just something more substantial than +X% galactic readiness.
What's interesting is the Author saying "But if its true (an incredibly big 'if'), then BioWare has pulled off the greatest feat ever: they indoctrinated us all." Indeed, maybe BioWare they just couldn't come up with what they considered a satisfactory ending, and so hatched a plan to essentially crowd source popular opinion of lore-valid options to release as DLC.