The decision in Legions loyalty mission is nothing like the ending of ME3 except in the most superficial sense that both involve some sort of choice. The context of the situations, the nature of the revelation involved, the significance of the choice are all completely different.
At the time we met Legion, we had just spent a game and a half fighting the Geth, who were actively waging a war against the Citadel races in conjunction with the Reapers. There was no question that at some level they were a destructive and dangerous enemy. Then we learned that this was only part of the story. This information challenged our assumption that the Geth were a homogeneous society, but it didnt contradict the clearly-established lessons of the story that preceded it. It expanded our knowledge of the situation without asking us to ignore the significance of what we had witnessed previously.
ME3s ending, in contrast, demands that we disregard everything the last three games have taught us about synthetic life. Its not a good thing when the primary motivation of your antagonist is revealed to be completely incongruous with the story you just told. The games go to great lengths to establish that synthetics are alive and capable of growth and selflessness and individuality and love just in time for Shepard to exterminate them all. Its like ending Pinocchio with Geppetto stuffing him into a wood chipper.
Were also implicitly asked to forget that this was never even the central conflict of the game. The Reapersand the heretic Geth, for that matter--were not our enemy because they were synthetic. That they were synthetic was incidental; it would have been the same had they been oozing, fleshy space-shoggoths. No, they were our enemy because they were trying to destroy and/or subjugate us. The battle of ideas at the core of the ME series was never organic vs. synthetic life, but rather indoctrination and subjugation vs. freedom and self-determination. Appropriately, this theme was even paralleled in the gameplay itself through its unprecedented emphasis on meaningful player interactivity vs. being forced down a predetermined path. Then they reached the end and inexplicably threw it all out the window.
Its just as faulty to compare the choices in Legions loyalty mission to the red and blue endings. Shepard never sought to control the heretic Geth. You can indeed argue the ethics of rewriting them, but you cannot claim it is the same as Shepard attempting to control the reapers after spending literally the previous scene (and ME2, if you were a Paragon) explicitly explaining to TIM why controlling the Reapers was insane and doomed to failure. Based on everything the game has told us, there is no reason to think attempting to control the Reapers will even work. Really, the best comparison for the control ending is not rewriting the Geth but rather Morinth convincing Shepard that hes so awesome and special that he can survive mind-melding with her. How did that turn out?
Likewise, destroying the heretic Geth was a serious and debatable decision, but killing a hostile enemy in wartime is a far cry from deliberately massacring your own allies to the last man after gaining their trust. A general might send his men into a dangerous and deadly situation to fight; thats a realistic ethical dilemma. No general of any conscience, however, would simply butcher his own men himself in exchange for an objective. Some prices are simply too high to pay, and he would attempt to find another way even if it meant losing. Without question Paragon Shepard would reject that sort of diabolical calculus. Even Renegade Shepard, who is no less committed to self-determination, would balk at being shoehorned into the Catalysts phony and obviously flawed paradigm.
This decision is not even a sacrifice in any meaningful sense of the word. People wrongly use that euphemism to describe Shepards arbitrary killing of the Geth, probably because it sounds nobler than alternatives like mass murder, but it is nothing of the sort. The Geth are not giving their lives. Shepard is taking them without their consent. As for Shepard himself, he is condemned the moment he enters the Citadel. Its never a question of whether; its just a matter of how. There is no feeling of choosing to give up your life in exchange for a greater good (as, for example, there could be at the end of Dragon Age: Origins) because your life is automatically forfeit, and its never clear that any of your choices even result in good, regardless. Thats not a sacrifice: its a gratuitous death sentence.
