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The Fury said:
                         

I always found that side of the story ending a little messed up. There was a war between organics and synthetics so in order to stop the war between such things happening again, a synthetic race wipeout nearly all fledgling organics and put them in synthetic bodies.... riiiight. A solution to the problem is the problem. I guess that is why the middle option was available. The middle option is the reason for the game.

Yes I find no logic in it but I quess that's because the theme of this ongoing cycle of war between synthetics and organics was just a plot staple. While playing through ME I thought it was about unifying races and synthetics against common threat. I personally don't find any of those options the reason for the game, they just dropped the ball.