I wrote a blog on this and this the crux of it. And before any snarky 'tl:dr' comments, consider that if you want to games to be art and thus to discuss them like they are, then you'll need to stop fearing large amounts of text, because that's what it takes to discuss art. If you only want to vent your spleen and be done with it, then discussing art isn't for you.
In order to break this destiny, the cycle represents the resetting of the universe. The advanced races are harvested to create the next Reapers, and the primitive races are spared so that they may flourish. The Catalyst appears immune to the paradox of its design, and presents Shepard with three choices -- yet all choices result in the destruction of the mass effect relay network, making communication and travel across the galaxy impossible. Whatever choice is made, the price is high. The longer he waits, the more lives are lost. The Reapers' goal gets ever closer.
What would we sacrifice of our ideals and morals in order or save the people we love, or to beat a deadly foe?
Act Three always ends in self-sacrifice. What the hero believes is his or her prize is often proved to be an illusion of the ego. This is why heroes must face literal or metaphorical death in the final moments. The fruit of their decisions may never be one that they themselves will taste.
Had Shepard defied the options before him, would a difference have been made for the better? Some people would rather die than choose. Yet is dying instead of saving, even if the latter requires great sacrifice, justifiable if it condemns the future? It is the question it presents us with now -- a terrible truth that heroes are seldom allowed full indulgence of their ideals, and quite often, they die vilified or unsung. The nature of heroism is by definition, a selfless service to the greater good.
As for the Catalyst's plan, that the only way to beget synthetic life is via manufacturing. Thus, destroying factories or self reproduction facilities would be enough to be reasonably sure no that more synthetics could be made. This is why the 'grey goo' scenario of nano-technology -- because scientists have already made it their mission to prevent unconstrained self replication.
Yet, organic life is a symptom of the universe -- an emergent quality of the universal elements. If it is assumed as inevitable that organic life will eventually, in some place, evolve, grow and create 'golems' of itself which in turn shall evolve as its rivals for existence, then the only choice available is to stem or impede the rise of organic life!
To the Catalyst, organic life is a stream that can never be stemmed. Synthetic life is an emergent result of that stream. Turning guns into landfill doesn't stop people making more guns and continuing to slaughter. I loved the seeming paradox of the Reaper Design. And honestly, when we live in a world in which nations wage war in the name of ending war, terrorise in the name of ending terror, oppress in the name of freedom or spill rivers of blood in the name of Divine love, how is the paradox of the Catalyst anything but par for the course?
The Reaper plan is not in place to stop organic life from enacting another Reaper plan. It's not the only solution nor the best, but why does that matter to the Catalyst? Remember, that regardless whether organics have invented autonomous AI or not, the Reaper purge is locked in place. By that time, organic life may have already risen and fallen under its own golems. The Reapers aren't there to prevent synthetic apocalypse but to simply limit its chances by keeping all life in a period of juvenility.
The existence of the Catalyst itself is very intriguing. Perhaps it's the end result of an ancient race now indistinguishable from synthetic, or was it their creation which ultimately destroyed them to save them, ala HAL from 2001. Already, the scenario of 'kill to save' has been used numerous times in the Mass Effect series, and at least once in the context of an AI run amok. And note that the rise and fall of the Protheans echoes the Reaper plan, ie an oppressive regime keeping other races from flourishing or advancing. In that case, the Protheans got a taste of their own medicine at the claws of the Reapers. If they had survived, who's to say they wouldn't have continued in their oppression to become just like the Catalyst and Reapers?
So for me, I saw Shepard at the end, thrust into a situation in which he truly had little choice. There was no chance that the Reapers would be beaten, and the Catalyst, through benefit of the Crucible, was able to offer compromise. It seems that the Protheans realised this and thus designed the Crucible for that purpose. Even if Shepard has defied the Catalyst, what chance would he and the other races of the galaxy had? Would they have waged a centuries long, losing, war like the Protheans did?
The ending of the series was true to the themes as I interpreted them. In fact when I got to the end, it all clicked. I had hoped for another way, but I realised the foreshadowing in the history and fate of the Protheans. The synthesis choice may well be foreshadowed in the very origin of the Catalyst itself. The concept of killing to save and all the hypocrisy involved within it, is a theme well used throughout the three games. EDI herself was once a deranged AI that Shepard had to vanquish.
I found the ending itself to be perfectly in keeping with the genre. Aurthur C. Clarke's 'Time Odyssey' series has a very similar premise, and if it wasn't for his Space Odyssey, nobody would be using the term 'Star Child' to refer to the 'Catalyst'. 2001: A Space Odyssey's Star Child was seen as a revelation, and yet its existence was almost devoid of explanation in comparison to Mass Effect 3's Catalyst.
The conceptual basis for the endings of both have clearly intellectual and moral foundations. Unfortunately this didn't connect to a large percentage of consumers, due certainly to a mixture of under-exploitation and a lack of being palatable. Yet 2001: A Space Odyssey, both the film and the novel, of which Mass Effect is inherently derivative, greatly succeeded precisely because of their varying degrees of mystery.
Yet today, it is a Twitter-Book Age, which has little tolerance for vagueness, nor any requirement to exceed the 'character limit' of one's most lazy intellectual effort. Add to that the mob mentality of the Net, the propensity for it to nurture one's muckraking, trolling side. The objection to the Mass Effect ending ended up completely out of proportion.
Mass Effect's interpretation of the Star Child and it's plan to both cultivate and manage life in the universe is not the flawed thing that is claimed. Although being god-like, it is not in fact a god. And despite being a synthetic intelligence, it is not an algorithmic one. Like us, its processes are heuristic. Even HAL9000 (in 2001), a cutting edge machine intelligence 'never known to have ever made a mistake or computational error' completely botched his assassination of the ship's crew, never mind that his attempt to do so clearly violated his stated intent, ie to 'protect the mission'.
As for the idea of god-like technology', Aurthur C. Clarke wrote, in his 'Three Laws': "Any sufficiently advanced technology is indistinguishable from magic." Yet that is definitely not to say that such technology is magical or has any of the perceived infallibility of something magical.
Mass Effect lore states that all A.I. became banned, galaxy-wide for its 'risk' of self-awareness. There was already one hundred year war going on between 'maker and machine'. Any adaptable, machine intelligence was seen as potential for future catastrophic war. Clearly the very concept of A.I. in Mass Effect does not entail any inherent perfection. An advanced artificial intelligence may operate beyond our own in cognition and mental capacity, yet imagine what humungous mistakes it could make if not simply a 'computation machine' but a real, living mind operating through a process of trial, error, pattern recognition and learning; just like us.
Those who believe the Catalyst to have acted 'un-machine-like' have not really grasped the series' philosophy on the subject, and that the motivation to create artificial life like the Catalyst must involve the emergence of an 'ego' and thus be contrary to the pulp SF cliche of the 'amoral, cold and calculating machine'.
The conceptual basis of the ending is sound enough, but the execution was lacking. I'm glad that Bioware are sticking to their guns on this and their execution is all they are changing.