The Catalyst says its creators made the Reapers, but that it gave them their "purpose", that it turned the creators into the first "true" Reaper (*ahem* against their will). Yeah... so it is an AI that turned on its creators and simply assumes that all other synthetics will inevitably do the same. It "preserves" organics by making them unwilling avatars of destruction, in the image of the initial species.
It still believes that synthetics will always destroy organics, and to prevent that, it... destroys organics.
So... why are we listening to this asshole?
And, via refusal, we learn that The Catalyst is Harbinger. Nice.
Why would the strength of the force you brought to Earth determine whether or not Synthesis is possible? Aside from that: if Synthesis didn't work for the Catalyst before because the organics were "unwilling", why does it work now when it would only get the consent of one man? Shepard speaks for all life? Everyone wanted it, really? Certainly having your DNA completely re-written suddenly, forcefully, and without your knowledge or consent wouldn't be physically traumatic or psychologically damaging in any way. Let alone the sheer mechanics of it. What the hell is entailed in Synthesis anyway?
Why would destroy be an option? If the Catalyst's purpose is to find a new "solution", and it doesn't consider destruction a viable solution... why would it let you do that? Why wouldn't it, once you fire at the power conduit, go all "so be it" like in refusal?
For that matter, why would control be an option? Even then, why wouldn't renegade Shepard rule the galaxy with an iron, Reaper-shaped fist?
The refusal ending doesn't really indicate if the next cycle didn't choose Control or Synthesis anyway.
Why couldn't refusal, with a high enough EMS, be the ultimate ending? Destroy the Reapers on your own terms? EMS doesn't matter past the "minimum" anyway, aside form the Synthesis ending (for some undisclosed and probably ridiculous reason). Why not refuse, and then watch your assembled fleets decimate the Reapers once and for all?
Even beyond EMS, nothing else you did matters because no matter what Shepard does, he/she ends up with the Catalyst and chooses a one of three "solutions" (or to take it up the ass).
Further, if the Reapers knew the Crucible required access to the Citadel, why wouldn't they turn off the freaking transporter beam?
There's an even bigger problem with The Catalyst; if the primary Reaper AI was in the Citadel all along, what was the whole "Keeper Signal" premise of the first Mass Effect game about?
Yes, these endings provide more explanation and closure, but they remain broken at a conceptual level.
I never bought into indoctrination theory, mostly because it doesn't address an even bigger problem. If the last 10-20 minutes are all in Shepard's head, it means he's still half-dead in London and the Reapers are still killing everyone. At least then we'd have the option for a better ending, but we wouldn't actually receive it.
So, meh, still a great game, great series, had a blast, will probably play through again a few times, but wish it had a better ending. I still love Bioware's work, and just wish EA would have left them alone. I don't want EA people to die or anything, I just wish they'd quit screwing things up.