The ending is Shepard, injured from the battle, fighting indoctrination by the reapers, and the entire scene is a hallucination. The Star-Child presents you with your three choices, and in the confines of the Reaper-dream, fighting back isn't an option (as you are not actually making the choices in the game's reality -- only in Shepard's dream). In real life, you agonize -- what's the "best" choice? Perhaps the Reapers aren't so bad after all -- perhaps they can indeed be controlled by Shepard, or perhaps synthesis IS the best option.
This is, of course, ignoring the fact that for three games, you have been told that the Reapers are evil, that they need to be destroyed, and that thinking any other way is a sure path to indoctrination (you can also see TIM and Saren -- both strong-willed men, by all accounts -- fall to their versions of the Control and Synthesis endings, respectively.) I don't think that it's any coincidence that the only ending in which you see Shepard alive is if you pick destruction AND your EMS score is high enough.
Now, let's say that this scene wasn't the actual end in the release game and you knew there was another 1-2 hours of game after this, and in the days/weeks before the game's release, people with leaked copies figure out the only way to proceed is if you have a high EMS score and pick the red button. We'd all do it without a second thought, and the effect would be completely lost. (How many of you used a guide for the suicide mission teams to make sure your entire squad made it out alive? I know I did.) But if this is true, it allows the player to experience indoctrination firsthand, unspoiled.
Is it trolling? I mean, yeah, kind of. But if this is the sort of ride Bioware's going to take me on, I'm OK with it. They're fucking with us, but I'm not so sure it's in a malicious way. They always try to involve the player in the game, to get them to make the hard choices, and letting them struggle with the effects of indoctrination in real life IS genius, even if they had to alienate some of the fan base for it.
This whole thing could be a bunch of desperate Biodrones clinging to hope, but I figure I'm going to be disappointed either way if I'm wrong, so I might as well drink the Kool-Aid. (That said, if they release the actual ending as paid DLC, I'm going to be mighty pissed because that IS total bullshit, but we all know how much EA hates the used games market -- I would be willing to bet a fair amount of money at this point that they have some free DLC up their sleeves.)
There are dozens of reasons supporting the theory in the almost 400-page thread I linked above, all of which make damn good sense, but I'm not going to bother to list them here. I was skeptical too until I read some of the thread.