Commander shepard, Saren ,and the Illusive man. Each of these three people aligned themselves with one of these endings; which in turn matched with their desires. Shepard wanted to destroy them this was always obvious. When it comes to the other two we see massive signs into this truth in the final showdown with each of these characters. The illusive man wanted to control the reapers but in a plot twist was instead controlled by them through indocturnation. Quoted saying "I warned you, control is the means to survival. Control of the reapers and of you if necessary" Saren is quoted saying "I've changed since then, improved Soveriegn has upgraded me. "You dont understand shepard there is a place for organics in the new world(....) the relationship is symbiotic, organic and machine intertwined a union of flesh and steel, the strengths of both the weaknesses on niether." I am a vision of the future shepard the evolution of all organic life this is our destiny. join sovereign (the reapers) and experiance a true rebirth" the three choices were actually just a test by the developers I think to see which charecters had the most influence on you during the games and in the cruel twist of them all having the same ending was the theme of the series and Shepard greatest fear. That no matter what you do you cant save everyone.