I know I'm in the minority here, but I just need to put this out there:
I absolutely love the ending to Mass Effect 3. Maybe I'm biased because I had my EMS high enough, so I was able to choose synthesis (which is, in my personal opinion, the optimum ending). I've seen so many people suggest that the destruction ending is the "proper" ending, because it is the only ending in which Shepard is presumed to be alive. While it remains true that Shepard is still alive, it is also the selfish choice - leaving the destiny of the entire galaxy hinging upon whether or not your own selfish attachment plays a bigger part is dirty pool, at best.
Mass Effect is no longer the story of Shepard. It is the story of us: the player, the characters, and all living things in the universe. Shepard is merely the avatar of this cycle; Javik himself makes that very clear. Hinging the quality and the character of the conclusion based upon the fate of a single entity, rather than that of all lifeforms past, present and future is a futile and worthless assertion. While I do give creedence to the argument that we have each spent 150 hours (maybe more) with Shepard, and having her die at the end seems counter-intuitive, Shepard has also been our avatar into the ME universe. It is *WE* who have spent all that time, and it is our decisions that have influenced that world, including this great and final decision we are given to make.
Many argue that the ending choice invalidates all the choices we have made up until that point - I patently disagree. I saw one commenter state, while referring to the synthesis ending, that what point was there in bringing the Krogans/Turians together, or the Geth/Quarians together, when in the end everyone becomes one big happy samey hybrid in the end? The answer being, simply, that you wouldn't have gotten there if you *hadn't* brought them together. The synthesis ending doesn't even become available unless your EMS is high enough; being poorly prepared and having not brought the galaxy to work together as a single entity would make this option unavailable. And isn't that the lesson this ending is meant to teach us?
Isn't that simply the point? That for millions of years, cycle after cycle, it's always been about races warring with each other. Synthetics and organics bashing heads and knuckles. The only way to keep it from spiraling into utter galactic destruction is to cull the cycle, much like harvesting your crops, to make room for the next cycle. From the point of view of the ego, it is easy to rationalize that the Reapers are evil and we are innocent sufferers. But from a high-level view, that of a praeter-human intelligence - whatever force the Star Child represents - this is merely a simple solution to a complex problem. They are disconnected from the individual sense of suffering, because they see it from a big picture. Remember when Garrus mentioned this? About how leaders have to disconnect themselves from the consequences to enact the greater good? This was their only response to the constant issue of synthetics versus organics.
But Shepard, as an avatar of your actions, brings an end to that. You bring together the organic and the synthetic (represented not only by the Quarian/Geth partnership, but also in that of EDI/Joker), and prove that the cycle need not end. You are faced with two selfish options: The first is to destroy the machines, continue a path of hatred and misunderstanding, and be doomed to repeat the mistakes in the future, but buy yourself and others a temporary reprieve. Rather than see the long term, future cycle, galactic big picture, we save ourselves (the most selfish choice of all) and everyone else living in the "now" without any concern for the countless future generations that will continue to be slaughtered and die in the war between organic life and synthetic life. The second choice is equally blind and manipulative, which is control. Take a lifeform with autonomy for itself, that was created simply with the purpose of enacting a greater plan which, selfish motivations aside, exists for the long-term preservation of life in our galaxy. Rather than attempt to understand, we seek to dominate. A force from sources greater than our own, and we fling ourselves into it, to take control of it as if it were a resource. Deprive it of it's own free will and operations, rob it of it's autonomy and soul, and subjugate it to our own selfish needs.
Or then, if we are lucky enough, we are given a third, glorious option. Synthesis. This option does not rob us of the choices we have made up to this point. Rather, it gives them validity. A singularity of man and machine, of synthetic and organic, is bound to happen. Not only is mention made of Shepard containing many synthetic components, but let us not forget the Reapers themselves - built upon the backs of harvested races for millions of years. They are not merely software and hardware, but also of flesh and blood, of DNA and RNA. Both forms of life seek to make the same choices represented in the binary options mentioned before. They are confronted with a form of life much different than their own, which brings in to question everything their existence stands for. They can either annihilate that alien life, or integrate it and control it. Subjugate it. Make it part of itself.
The idea of spiraling toward Singularity is ever present for both sides. So do we, as organic races, continue stumbling toward this inevitability with awkward, selfish and misunderstood steps? Do the synthetic races do the same? Or do we end this hatred - this cycle of domination and destruction - and bring about the peace that Shepard, as an avatar of all humanity, has worked so hard for? The very synthesis of man and machine that Shepard, herself, represents. The future hinted at in the love between Joker and EDI. The future that can be build on Rannoch between the Geth and the Quarians?
Pulling allegory from the Bible, I am reminded of the story of Eden. This story is often misquoted in that man eats from the Tree of Knowledge. If you've got a Bible, pull it out - man eats from the tree of the Knowledge of Good and Evil. In a pure, blissful form, there is no distinction between these notions, because they are artificial constructs of a prejudiced mind. Good and Evil are merely relative of each other. To destroy these distinctions is to create perfect thinking, which is what man experienced in the Garden of Eden prior to the Fall. If we cease to distinguish life forms based upon what atoms they are made from, and instead simply embrace life as what it is - life in any form - can we move from all this hatred and fighting, and all these attempts to dominate and control each other?
If all forms of life are simply "life", in whatever complex form we can define, then we can truly start to be at peace, rather than repeat the selfish mistakes of tens of thousands of cycles. Isn't this what Shepard has fought for all this time? Isn't galactic peace, and a harmony between lifeforms really what it's all been about? Every attempt by either a synthetic or an organic life form to attempt to use the other side for selfish means, or for the means of manipulating one's advantage over the other, ended badly throughout the series. Because the selfish choices cannot be the ones to motivate us, or we are doomed to continue repeating these cycles of extinction.
It is only by selfless choices and actions that Shepard is the first organic to ever be offered the choice of how to take things. Only in that aspect has the galaxy ever been ready to take the step toward harmony. By patching all that hatred, prejudice and distrust, and by showing the powers-that-be that we have evolved past the cycle that was needed to keep us from destroying ourselves, are we now given the ability to move forward. Shepard's selfless choice to throw herself into the Crucible and synthesize all living things, synthetic and organic, seems to me the culmination representation of EVERY choice she made along the way. It's the big payoff, and in a BIG way.
To minimize this choice as being inferior simply because it results in her death is poor thinking, I believe. Isn't the death of one worth the continued harmonic existence of billions? Trillions? The end to a cycle of hatred, opposition and war?
This series couldn't have ended in a more magnificent way. I know that there are people out there who felt disappointed in this ending (I'll concede that palette-swapped ending videos are a cheap way out), but perhaps if you reconsider the point of your Shepard's actions, you might feel differently. And I know I speak for only a small group, but since BioWare is listening to our feelings about the ending, please keep in mind that there are people who liked the way it ended. If you choose to explore the ending in more detail or provide additional closure, please consider doing so in a way that doesn't ultimately change this initial experience. Make it optional. Because for some of us, this saga couldn't have ended on a more poetic, beautiful note.