The whole game, 1-3, is about Shepard making decisions for the entire galaxy. Why is the fact that every one is forced to live with his choice suddenly bad? Also no diversity is gone because Shepard post Mass Effect 1 is exactly what synthesis creates. The problem is you are approaching this like a Human instead of like a synthetic life form. Being the same does change stuff.I perfectly understand the green option. I understand free will isn't affected, but Shepard making the choice does absolve all free will, in that you make the decision for everyone to become that new framework. But the diversity prior to this event happening is gone. Regardless, do you really think organics would accept synthetics now if they didn't before? The geth are still created, no matter them being equal now. And this might be going over the line, but both white and black people were born, yet white people enslaved black people. Being the same doesn't change sh*t. People always find a reason to cause problems. Synthetics might not destroy organics anymore, but this android/cyborg/organthetics/synthganic faction would have trouble with another faction and they would obliterate eachother.
The cycle was never about finding a way to create peace. The cycle was about finding a way for Organics and Synthetics to not always end up at war. The levithans (and later the reapers) saw this play out time after time. That always one would fight with the other because of the a lack of understanding. You can see this difference of view points in how EDI talks about how she is starting to gain humanity during her idle talks on the ship. Every option still leaves open the possibility of wars and crime but it won't be just because X is a computer. You'll never see a conflict like the Geth and Quarians again because the fundamental reasons for that conflict won't happen.
You answered you own question. An epilogue happens after the ending. In the context of Mass Effect 3 the epilogue is whatever we choose to imagine after the the game ends. You don't change anything about the endings you just create what happens after the ending. For example I like to think that the Story teller and child are descendants of my Shepard and his Love interest. Or I think of the Story Teller as the manifestation of Reaper Shepard (cause I choose blue for my favorite/cannon ending) and he is sharing stories with some one in the galaxy (It might even be virtual in some sort of matrix like reaper program for learning)What really is the difference between an ending and an epilogue? An epilogue happens after the end. But where does the end end and the epilogue start? The IT doesn't start after the ending of the game, it starts before Shepard even reaches the Citadel; it is part of the ending of the game. It's just a way of interpreting it. Wether Bioware intended for that to happen or not, I couldn't care less. The IT gives me a more than acceptable ending and allows me to create my own perfect epilogue that I am extremely satisfied with. And again, if they did not want me to do that, they shouldn't have made those 'mistakes' and shouldn't have made the endings so vague.
Part of the ending isn't the ending. You are rewriting the ending because you refuse to follow the story as Bioware is telling it. Why not just go back to Mass Effect 1 and say the true ending is Shepard dying at the beacon on Eden Prime and everything is just glitch of the beacons memory transferring systems? What other parts of the story did you just rewrite because you didn't like it?
They aren't mistakes they are just random events that you choose to great irrational connections and explanations for why they must exist. Or some of them could just be mistakes in textures and art models. Programming bugs do happen.