The main conflict between Shepard and the Reapers is NOT Organic Life vs. Artificial Life, the main conflict is the Reapers want to destroy EVERYTHING. The Geth will NOT be spared by the Reapers, they are (to the Reapers) just another race to be used and then discarded when of no further use like anyone else. Those who try to serve the Reapers willingly are ALL doomed to die because the Reapers DON'T CARE!!! It is made clear that ALL life will be destroyed by the Reapers and anyone who thinks the Reapers can be reasoned with or that they place value on certain life forms are deluded and will be killed or harvest like everyone else...
And then comes the Ending of ME3 which goes "Nope this is all about Organic vs. A.I. and the Reapers are trying to make peace by killing everyone... Because you THAT makes sense!!!"
The point of everything leading up to this moment was that the Reapers were coming and that we needed to work together or try to survive at any cost to stop the Reapers. THIS is the main theme of the 3d game, stated at the start by you. And then the ending tosses that all aside because the developers decided to just redo the Quarian/Geth war only now with a Little Blue Troll who gives you one of three choices and tells you that you were wrong about what the game was about and that it's really about THIS thing.
Have I mentioned that I hate this ending? I hate ending.
![Evil or Very Mad :evil:](./images/smilies/icon_evil.gif)