It's kind of like how they expected the ending of ME3 to make people think in all sorts of ways, and it just resulted in an angry fanbase. That wasn't even touching on a touchy social issue, that was just the end of a game. The writers must be very careful when handling pretty much anything, lest blowback occur.
The main issue with ME3's ending is that it insulted the intelligence of the player by expecting them to accept its ludicrous and ill-designed premise.
You know that colossal space microphone we've been building? We have no clue how it works, but we're going to use it anyway. Okay, it's plugged into the Citadel. Holy crap a space kid appears out of nowhere. It's telling me it is the Citadel, the leader of the Reapers AND the Reapers all at the same time. If it's the Citadel, why didn't it just just open itself to Sovereign before? Why did they need Saren or the Conduit?
Now the space kid is offering me three options - destroy the Reapers, control the Reapers or turn everything biological in the entire galaxy half-machine and upload LOVETHYCREATOR.exe to all synthetics. Ignoring for a moment how each of these options work on a technical level, how did the space microphone's engineers not know about these functions when they built it? Or are these functions of the space kid? Nope, the space kid just told me it was the space microphone that changed him to enable these options, and that he didn't have them before. But wait, now the space kid is telling me the space microphone is merely a crude power source. So which is correct? How did a simple, oversized battery give the space kid options he did not have before?
The space kid is telling me these are the only options, unless I want my civilization to fall. It also tells me his cycle of extinction will no longer work. But this space kid is the leader of the Reapers. Why should I trust anything he says? We're enemies. His 'options' could easily be traps to kill me so the Reaper invasion can proceed unimpeded. Can I argue against him on this point? Nope, I'm not allowed to do that. I'm forced to assume that this space kid, essentially my archenemy, is telling the truth.
Okay so to destroy the Reapers, I need to... shoot at some tubes? Wait, what? How is that going to direct the space microphone's energy at the Reapers? And how does this energy destroy the Reapers, exactly? Is it some kind of directed EMP? Or is it some kind of advanced software virus? How did the engineers not know about this? Also, destroying all AI's indiscriminately? If it's specific enough to target only AI's instead of all technology or even all forms of matter, why can't it be made specific enough to target only Reapers? As Legion showed me on Rannoch, the architecture of Reaper code is considerably different from other types of AI. Not only that, I happen to be in the possession of a Reaper IFF, which should make it considerably easier to target the Reapers only. Still doesn't begin to explain how shooting the tubes accomplishes any of this.
The second choice is to control the Reapers, I need to grab on to a pair of electrified handles and... disintegrate. Okay then. Apparently this will give me control of the Reapers while also killing me, which makes no sense. Or, as the space kid tries to imply, it will use me to create something in my image that controls the Reapers. First question, what part of me is necessary to create this Reaper controlling image? Do I HAVE to be disintegrated for it? Can't I just wear an advanced electrode cap and have it copy my brain and let the brain AI copy rule the Reapers while I go back to my love interest and my friends and enjoy some well-needed R&R? Also, how can I trust that this copy won't just betray my ideals, obey the space kid and continue the cycle? And even if the AI copy did stay true to my ideals, where would the space kid go after my copy takes over? And why would the space kid relinquish control of the Reapers in the first place? Will my AI copy control the space kid as well?
And the third and final choice, uniting organic and synthetic to end the eternal conflict between organic and synthetic. First of all, how is that going to end hostilities? Unless it causes galaxy-wide brain washing by suppressing any dissenting view or opinion, organics opposed to synthetics and vice versa aren't going to magically change their opinions because they're now full of tiny nanomachines and copies of LOVETHYCREATOR.exe, respectively. And if it does cause galaxy-wide brain washing, is everlasting peace really worth it if it requires the wholesale sacrifice of freedom? And the transformation itself, should people not be given a choice? Should peace come at the cost of self-determination? Moreover, how does this even work on a practical level? How does the space microphone infuse organic molecules with nanomachines? Even if they're incredibly light weight it's still the matter of transforming the collective biomass of an entire galaxy in the matter of a few seconds. There is just no way that the space microphone holds that much building material... and even if it did, the rapid change would generate so much waste heat that all living things would disintegrate. And how exactly does me jumping into a beam of energy and disintegrating cause the space microphone to transform the entire galaxy into organic-synthetic hybrids? Being full of cybernetics does not make me a walking blueprint.
Nah, I don't trust any of these options. How about I just shoot the space kid and try to find a way to use the space microphone without him? Oh look, now he's mad and talking with a Reaper voice, telling me the cycle will continue even though he just said not five minutes ago that the cycle no longer works. For whatever reason I just stand there, looking solemn doing nothing while my civilization falls but Liara's underground USB magically enables the next cycle to defeat the Reapers, so I got that going for me, which is nice.
This ending is built on a broken wrists-level of shoddy handwaving and for some reason BioWare thought it was not just going to fly, but inspire high-level intellectual speculation among the fans. Self-delusion on a truly remarkable level.