To be specific, the emotional reaction that Mac Walters and Casey Hudson managed to provoke is exactly the same reaction that you get when a really close game of sports between two teams that have heavily invested fans... suddenly ends with a third team that doesn't even play the same sport is given the win.
And the referee team responds to the heavy criticism by saying, basically, "You're just spoiled fans. They're athletes too!"
What Bioware did with this ending is completely ignore the themes of the story *as had been developed* through the series, and substitute the themes as written in the margin notes of a design document that had been discarded during the development of the first game.
They laid the groundwork for an ending that celebrated victory through diversity and strength through difference.. and then ended the game by focusing on a secondary theme as interpreted by a poorly programmed AI.
Basically, they didn't write the ending to the story they'd actually written. They wrote the ending to a different story. If it had ended with Shepard and Anderson watching Earth while the Crucible fired.. that was the natural ending to the story. That was it.
Instead, Mac and Casey took subthemes that they hadn't really touched on, i.e. synthetics vs organics and the 'supposed' inevitability of one destroying the other, and made that the ending. Before you say 'but the Reapers!' let me remind you the Reapers aren't 'really' synthetics according to Bioware's writing. They're some kind of synthesis of organic and synthetic. So yeah.. machines vs people? Not actually the primary conflict.