I can't stand a lot of things about the ending and the Starchild's logic isn't what is on the top of my list. Though why the god figure that controls the Reapers would give this random human the choice to undo what he has administered for eons seems far fetched. But okay I'll go with it. His circuital logic about making synthetics to kill organics to keep synthetics from wiping out all life instead of half of it, can make sense in a way. I'm sure the race that the Starchild belong to thought it was their best option, but it is arrogant for them in their time to believe every single cycle after them would end the same way. If synthetics completely destroy all life, from the advance to the birds and the bees then they are right. But they set this plan in motion before they had the insight of eons.
The Geth have already proved to be the contrary. When the Quarians left Rannoch, the Geth did not turn it into a machine paradise, destroying all life on the planet. Hell they didn't even live on Rannoch, Legion tells you this much in ME2. He tells Shepard that the Geth have been acting as groundskeepers for Rannoch, making sure it flourished. For the Starchild's people to start this cycle robs all races that come after them the freedom to try and fail on their own is unfair.
Here is an anology, I'm eating steak with a steak knife and someone takes that steak knife away from me because I might cut myself. Sure, its very possible that I might, especially if I'm being risky with it. Something with AI, if organic are risky with AI, than yes there is a very good chance that they will destroy all life. But that is exactly one of the themes of the ME series. AI have always been a problem in the storyline and Shepard is there to guide organics and AI to either war against each other or to make peace.
On Rannoch when Shepard talks the Quarians down from attacking the Geth when Legion was uploading the Reaper code, I felt proud. I felt like I had done something good. I felt like what Shepard had been doing, the actions she had been taking mattered. I could feel the weight of excellant story telling. However, the ending completely undoes that. It striped down that beautiful moment into a War Asset number that doesn't matter in the end. I could have easy said **** it, killed the Geth or the Quarians and played a couple hours of MP to get my numbers back up. When story elements mean nothing in the end I call BS. Shepard can't point to the Geth fighting along side the people they have been at war with for 300 years and say "Look! We are working together. We are not making the same mistake your people did." Yes, in the years to come there will probably be another war with synthetics as there will be war with organics vs organics. Conflict is natural, it will happen over and over again, you don't need synthetics for that to happen. But killing everyone because you don't think they will be able to get along is wrong.
However, I can actually let that all slide. I can accept the Starchild's logic. My problems begins with Shepard's lack of strength at that point. What happened to Commander Shepard? She completely accepts Starchild's arguement, right or wrong. At any other point in any of the games Shepard can disagree/agree or follow/rebel with pretty much everyone. Sometimes Shepard's logic doesn't make sense but that is the point. You can kill the rachni, you can save the rachni, you can rewrite the Geth, you can distroy the Geth. Right or wrong, sense or none, good or ill Shepard has choice. You can choice to make the wrong decision based on role playing of your Shepard.
Let's say for a moment that the Starchild is completely right and these choices are the only options you have to stop the Reapers. Say everything is at face value and that there are no hidden meanings or manipulations going on at this point. Why can't Shepard be wrong and say "To hell with you, you control the Reapers, you can turn them off. Do it." What happened to the Silver Tongue Siren that can charm Krogan, persuade truians, and captivate her people? What happened to the woman who talked Saren into shoting himself so that she could stop Sovereign. She apparently died sitting there next to Anderson because the woman who went up in that beam of light isn't Commander Goddamn Shepard, the woman who head butts krogan, punches Yahgs in the face, and controls armies with her word. She is replaces by someone who nods her head, says okay, and meanders toward horrible, depressing ending A, B, or C.
Putting that aside too, even if you 'save' Earth with the best possible ending with max War Assest, Earth is still boned. This takes place a little less than 200 years from now. Right now we are trying to find alternatives for fuels and other resources. Thane talks about his planet and that thankfully us humans were able to get off our planet before it became a major problem. Now we are struck back on Earth with a little less than twice the population we have now even if the Reapers kill a billion people. Add if you cured the Genophage then Earth faces over population of krogan. Add Rachni in there too if you saved them. The Truians and Quarian might not starve if the Quarians brought their Liveships with them. But how many of them were destroyed in the fight?
This is also assuming that when the Charon relay that orbits pluto doesn't destroy the Sol system even thought the lore clearly states over and over again that it should.
But what the icling on the cake is the crew, why in god's name would I want that fate for them?! Here is the thing, assuming that they are forever trapped on that planet. They might survive three, maybe four generations but they will all die out eventually. To maintain a poplulation you have to have 10,000 people at least. This takening in deaths before procreation. The Normandy who's only crew is those who just happen to be aboard at the time the Reapers attacked Earth is maybe 20.
You can look at the success and failure of the orginial American colonies to jugde where this is going. And those people arrive at least semi prepared. The Normandy crew has no supplies other than war time equipment. Those on board are soldier and scientist at best. If I can go ask some random person on the street where eggs come from and they tell me 'the grocery store,' I have little hope for them. This not mentioning the crew who have medicial problems Joker for one has Vrolik syndrome and even if you pick the Synthesis ending you still see Joker limping as he get out of the Normandy. Without the advanced medicial attention of their time he will die. Kaidan will also be in poor health due to his L2 implants with out the aid of pain medication. (If he is alive in your game, of course) This is all counting that no one died in the crash landing. And assuming that everyone magicially made it back to the Normandy when they all turned coward and abandon Shepard in her moment of need.
Aside from the plot holes that make swiss cheese look solid this ending is so bleak and dark. The implications of what happens to the characters we have loved since ME1 is heartbreaking. I rather have the scene to have went black and Shepard waking up on the Normandy after Eden Prime implying that the events of ME1, 2, and 3 were all dreams.