Oh, I know that. That's what I got in my first run. The point is, everything after the Shepard being hit by Harbinger was all an illusion by Shepard's indoc process. There's really no other way to explain why Shepard is still amongst concrete rubble in a breathable environment when the Citadel exploded after the destruction choice.
It does kind of make sense that the other two options, merging with synthetics (THEY DON'T HAVE DNA!) and controlling the Reapers all mean you've accepted machines in some way and wiped out your own existence, hence being fully indoctrinated by the Reapers. And since the god child tries to tell you that choosing destruction will kill you and destroy the mass relays, it's not that hard to believe that this is not what the kid wants you to pick. It's been shown in previous Mass Effect games that anyone can fight indoctrination if they're strong enough.
Also, the Crucible should have been a trap... Maybe it still is.
All good points.
One thing you have to give them credit for (including the ending)... It definitely leaves a lot of room for analysis, speculation and debate. Much of it quite dark and unsettling. That's what good Sci-Fi does. Maybe that's what they were shooting for... the mindf^* k ending that leaves you in an emotional and philosophical conundrum. I know that's not what many expected... or want... but if that's what BioWare set out to do then they definitely did it, probably more effectively than they hoped. lol