Ok, so I FINALLY got to finish the game. I totally understand why some people could get upset. Personally, I thought the ending was perfect (assuming this is the last installment of the series). My choice was obvious to me..
(Red)Choosing to destroy all synthetic life (along with myself and presumably EDI) did not seem like the right choice. EDI was able to think on her own and begin to have emotion (The Geth you saved showed this also). So, if our future children developed Synthetics that would/could eventually "destroy" us..there is no certainty it would happen. After all, Shepherd already proved the Catalyst wrong by living.
(Middle) Synthesis seemed to be a popular choice for many. My problem was that there should never be an end to evolution. We shouldn't "play God". It is not for us to decide every being's life. If everyone ended up being the same, there would be nothing to learn, no triumph or adversity. Nothing to feel "alive." Destroying all the Mass Relays would be completely detrimental to everything Shepherd accomplished (ending wars between feuding races (i.e. Krogan and Turian).
(Blue)This one made the most sense. Sacrifice myself to control the Reapers. Humanity can carry on. Evolution continues. Yeah, I guess in a way it sort of sucks dying..but to me, it was the most logical choice. In the end, Shepherd still became a legacy and hero.
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XBL and PSN: Shad0wn9ne