In the end, both sides, synthetics and organics, achieve what they strive for. Organics receive the unmatched brain-power and knowledge that synthetics have. Synthetics receive an "understanding" of the world they live in, and the capacity of true intelligence (i.e. morality, preferences, emotions) that Organics have and that EDI and Legion achieved. Through this, both forms of life receive what they wish for, and, in addition, the Reapers share the knowledge of all the past cycles with us. Even though Shepard dies, it is in a way that sends the galaxy into a new golden age.
If anyone has any quarrels with my reasoning, please let me know, I want to hear others' opinions.