Good read, here's my own personal take on the ending:
I think our last fight was fighting the indoctrination process. If Shepherd raises a credible threat thus proving his mettle against the Reaper's machinations the other pro Reaper options are opened in an attempt to bring Shepherd into their fold. He proves usefulness as an intelligence for them to leverage rather than as mere puddle of DNA. Throughout the journey Shepherd is haunted by the kid from earth whom only he has acknowledged as real. He wakes from these dreams seemingly with headache pain. The dreams play on his greatest fears of failure slowly narrowing his perspective. This narrows his resolve, but it also makes him more predictable and therefore more easily manipulated. The final scene plays out with him dazed listening to the king of Reapers with little question or protest. In fact his questions and protest dwindle all the way to the third option of synthesis where a seemingly bewildered Shepherd mutters a weak I don't know. The only option where shepherd can possibly live is the destroy option. The Reaper god presents it as the most pyhrhic. It will destroy the geth and your friend EDI, which will be very disappointing to Joker, and it will not end the cycle. And if your EMS score is too low it is for not. Earth will be destroyed. The other two are much more favored in the Reaper's presentation and smack of ruthless temptation that speaks to shepherd's renegade or paragon nature. To be honest although there is the possibility of three choices there is in this reading only two. Two are Reaper arguments and one is to stand against them. If Shepherd chooses Synthesis or Control he is following the Illusive Man and Saren into the same logical traps that the Reapers caught them in. The desire to be powerful, the desire to cooperate and prove your right to exist before the unsympathetic intelligence of an amoral machine god. An exercise in futility.
As for the rest of the magic show in this case is how the indoctrination process resolves itself in Shepherd's mind. In the case of indoctrination Shepherd is incorporated into the machinery of the Reapers and is kept contented that his act has brought peace to his friends while his will and body are co-opted. In the choice to fight Shepherd find's a safe place in his mind, his hopes, to shield himself from the tortures of the Reapers. Much in the way that the main character from Brazil goes off into that flight of fancy when he is being tortured.
If Shepherd has enough EMS he wakes up to continue the fight to the end. If he's indoctrinated the whole galaxy tells his tale of how he led them to ascension in the belly of a reaper living out a reality beyond our comprehension. They are each a nation unto themselves afterall. Either way he is a legend.
Reaper Motivations
Much has been made about the Catalyst's revelations. And frankly I find his reasons to be not credible nor do I are we intended to think so. The Reapers have no reason to explain themselves to us, nor any investment to be honest with Shepherd. Instead the Catalyst offers up something the Reapers think Shepherd wants to hear. Shepherd at this point is tired of war. He has lost his friends, his homeworld, and sacrificed bits of his own humanity to get here. The Reapers offer him an easy out. They make the case that they want what he wants: peace and galactic safety and order. And if he plays there game they will trouble the galaxy no more. Since he is a soldier he understands conflict best of all. So the argument is centered around the eventuality of conflict. In this case between organics and inorganics to types of consciousness that are as alien from one another as is possible. Through that the Reapers pose themselves as a solution to conflict as he has been a solution in his own galaxy. This is all to bolster their credibility with Shepherd. To speak to his sympathies and better nature as a character who understands war, sacrifice, and survival. It's a load of horse**** but Shepherd is too weighed down by his survivor's guilt and fears to see anything other than the possibility of hope being dangled before him.
The Reaper's actions show the opposite of sympathy for organics, though. As Mordin points out Reaper tech design for their organic components and collectors show utter disdain for organic needs. They are cultureless, unimaginitive, and sadistic. Sovereign refers to organic life as a virus. A virus to them that is necessary to cultivate, but more ever, neccessary to control. They had painstakingly stocked the universe with a path of technology that would manage growth and lead spacefaring peoples to the their Citadel. From there the voice of indoctrination can subtly guide the decision makers of the galaxy toward acts they see desirable for their next harvest. They indulge no sympathy, tolerate no dissent, and give no quarter.
Yet within the design of Reapers there is a paradox. What is a Reaper but a the indoctrinated corpse of a nation of people? How can such a thing be independent? Answer, they aren't. Reapers are the essence of amoral determinsm. They are the mad gods of Lovecraft. Inexplicable. The only thing they stand for is the neccessity of the cycle. The neccessity to continue existence. The neccessity to manifest it's order for the order's sake. Justification is unimportant to them. They are the pinnacle of sycophancy. They stand for nothing but the order they serve as an ideal unto itself. An order imposed so long ago that it's purpose and spirit is lost. They are the police state that cannibalizes it's own citizens for the sake of self preservation.
Life however is always a threat. Because life is a struggle to manifest itself with freedom and independence. Throughout the game Shepherd champions this struggle whether it's helping the geth be free to self determinate or it's handing the krogan back their right to flourish as a race. Shepherd's main contention about the reapers is the fact that they wish to impose their judgement on all races. That their will is to be forced on ours. Shepherd desires a universe with a valid choice. Reapers desire a universe that only consists of their choice.