Hm. Let's say the whole Catalyst thing is symbolic, in Shep's head. He, in fact, has become the Catalyst. A catalyst is something that facilitates a reaction, but does not take part in it. This last distinction is important: most people think of a catalyst as "extra fuel" that gives a boost. This is not correct. A Catalyst can alter the environment a reaction takes place in, altering the reaction, but not being consumed or itself reacting.
So. I think Shepard is the Catalyst. He has become one, by doing what you've done as the player: setting pieces in place, mediating disputes, forming alliances: he has altered the environment.
The three silly choices are symbolic as well, and not literal. Instead of "the action to take right now," it is "the future you choose." In this context, the broad choices almost make sense.
Will you dominate synthetics, and slave them to your will?
Will you destroy them outright, and abolish them from the galaxy?
Or will you work towards a harmonious future - one shown literally in the final scenes, but really meaning only a desire to work together, as one people, as all sentients?
If this is valid in any way, then the "real" ending hasn't happened. Shepard really is zonked out / still in that beam / anything, really, no indoctrination needed: I think this has potential as what Bioware may have had in mind. It's not the Reaper conflict Shepard pushes the green/red/blue button on, but his own doubts, his own choices, the conflict in his own mind, his guilt and regret over not being able to save everyone.
However.
Even if this is true and I have somehow nailed an insight into their intent, this has been handled so so horribly wrong. Even if some bizarre choice to let us actually finish the game later was made, SOME HINT in-game via ingame mechanics should have been there. The passive, nearly choice-less ending sequences ... dumping you out with a "BUY DLC!" advert and plopping you at a save point before the Cerberus assault - is just waaaaaaay too jarring. Could have been done infinitely better.
I may, of course, be projecting all this. But. If I was writing this, and that wasn't really "the end?" That's what I'd have done. That's what I'd have made it mean. Maybe he's really just passed out in front of the control panel from blood loss, next to poor Anderson. Who, frankly, might not be dead either.
We'll see. I feel like I'm on to something, but who knows.