Jesus Christ you guys. If only I'd have known I would be walking into WALL OF TEXT ALLY today, I would have put on some tea.
The problem with the ending, aside from the nonsensical nature and sudden reveal that higher power is at play, is more to the point of a lack of closure or sense of what is going on. The reason the Indoctrination Theory is so prominent and favorable, no matter how utterly not true it will eventually turn out to be(Big supporter myself, but the fact that we want it to be true just goes to show that it won't be), it gives us the idea that Bioware are still capable craftsmen.
After the Dragon Age II incident, fan relations with Bioware are not good. And then here they come, writing this genius project that is probably one of the best games I've ever played, only to come out of nowhere with this problem. This problem is the ending. It disconnects us from the universe they have created. No longer are we Shepard, fighting the good fight, trying to do what's right, beatin' down Reapers like. KID. DYNOMIIIIIIITE. Now we're in a position of total control of the Reapers. We have been summoned by the Architect. We're in his white room, being told that everything we thought was wrong, and everything we believe is a lie. It's not about the concept we have of "fighting", or the idea behind "destruction". It's suddenly about chaos and order. What is is what will be, always and forever. This conflict between Synthetic and Organic. The conflict that will always end in total destruction between organics. The conflict that will always see the Synthetic victor.
And then there's the means of an end, which is to destroy all Synthetic life, of which you see the negatives, as the synthetics aren't our enemies, the Reapers are.
Controlling the Reapers is never explained because it's almost as if Bioware knew that it's the statistical solution. We control them in this ending. That is fact. So, how much can we control them? Do they follow our will? Do they seek the rebuilding of all planets destroyed in their war? Or is our control only limited to "Yo, get the hell out of here"? If not, then this ending is easily the most positive ending, as we can just tell the Reapers to go and rebuild the Mass Relay's, and repair all of the damage they fixed, only to sit on the sidelines, keeping a watchful eye of this "Synthetic rebellion".
Or Synthesize, which forces total homogeneity across every living being, animal or not, to be the ultimate balance between Synthetic and Organic. It's morally wrong in every way, which is strange as it is hailed as the best ending, requiring the most EMS to get.
The problems with these endings are how nonchalant they are. Not only does our decision to spare the Geth and use them to their merits and let them build their own path in peace and harmony, but also EDI's thirst for knowledge and understanding as she experiences the human condition from within her own circuitry. If you choose to let the Geth keep the Reaper code, they spark life. True, life. It's not explained any more than that, but as Mass Effect 2 pointed them out as "True Virtual Intelligence, real synthetic life", it's heavily implied that they are living more so than ever. Even more so with their own independence. That's the most striking thing about the Rannoch sequence, you can give the Geth(Allow, really) independence. So now you have something you've never had before in their culture; diversity. Networked together as all machines usually are, Geth 23223232 will now have a different opinion, stance, view and outlook on things than Geth 23223233. In time, their people will flourish and blossom into something the universe has ever seen before.
Synthetics, yes, but this sequence went so far to imply that they were people now. Instead of "We" and "us" it's "him" or "me". Individuality. The chance to live for themselves. This sequence implies that they are, in time(if not already), going to turn out like every other species; as diverse as they are populated. So when the end of the game rolls around and groups all synthetic life together in this lump of hate, it's presented in a way that makes no living sense. We are not allowed to interject that the Geth are now a people, more so than ever before, and that it would be impossible for them to one day decide to group together and wage a campaign of total organic destruction. It makes no sense. They valued life at the very beginning, deciding to force the Quarians offworld so they wouldn't have to kill them. And here they are today, this rather peaceful people who never wanted to fight, they only wanted to survive. But it doesn't matter. It doesn't matter that EDI would rather harm herself than another person if she could help it. None of it does. Our decisions are meaningless.
"Synthetics always rebel against the creator? What about the Reapers? Take a look at the Geth! Look at them! They're helping the Quarians move back into their homeworld after decades away. They are forging friendships across species and becoming more diverse as the day goes long! Everyone said, oh, well we have to kill the Geth, we can't take that risk, we don't know what they're capable of. But I do! I've seen what the Geth have to offer, I've seen what the Geth have always wanted. They've wanted peace, acceptance, a home. And they were willing to spare the Quarians to prove that point. The Geth aren't our enemies! YOU, are our enemies!" Where was that dialog option? Where was my chance to show the little ghostly bastard what progress I've made? It's nowhere to be found. Instead, we are being told: The Synthetics, all of them, will rebel, without second thought, as they have always done, as they will always do. With so many plotholes to back it up that I can't believe that.
And then there's Synthesize, which is almost a paradox in itself. You tell us Synthetics will always, always rebel against the creator, yet by making every living half synthetic and half organic is supposed to fix that? How? What about when we create V.I's again? What about when we build more robots? Or YMIR mechs? Loki mechs? What about my goddamn space hamster? What's he going to do when his little precious self turns half robot? The fish? Um... here's one for you... what about reproduction? As evident by the very ending of the game, with the Stargazer, there's a child there. How is he synthetic? Test-tube babies are the perfect example of this. They are, essentially, built by machines, but by using organic matter and putting it in the same conditions that a human body would have been able to provide, and they are organic. How does a half-synthetic person suddenly give birth to half-synthetic babies? Sure, I could be nitpicking, but that's what I'm talking about.
You present the option to not only keep the Reapers, but also fix ourselves so they will no longer slaughter us(Harvest, blahblahblah, I didn't see a single human Reaper in ME3 so they can shove it... aside from THAT human Reaper I mean) and cause this perfect harmony between us, but it doesn't make sense. Certainly, in the shortgame it makes some semblance of sense, but in the longrun it doesn't. The problem would be back immediately and put us in an even worse position because we are machines, willing to be reprogrammed by a higher-power, vastly superior to us. At that point, hell, we could all self-destruct and kill ourselves, preventing the Reapers a chance to do so themselves. Or maybe the Reapers would "toy" with us by using our synthetic brethren as Husks as they did during the events of ME3 and kill us off faster.
Maybe I'm going to far with that, but if I can poke ANY sort of hole in it, then clearly it's not very good. Destruction is the least satisfying, but most probable ending in the game, but the way the Catalyst talks about Synthetic life makes EDI and the Geth redundant anyway, so really, it doesn't matter what ending you get. The question you should be asking is, what's my favorite color?
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