I feel like with all the choice given to you throughout the series, Bioware had to eventually converge onto one conclusion. And that they did. Whether you believe Shepard was indoctrinated or not isn't the point. In the end, shit happened and everyone died or they didnt die. What matters is that throughout the entire game, Shepard was able to solve the galaxies biggest problems. People making robots that eventually rebelled, assholes creating the genophage, and multitude of other shit. As the reapers themselves stated about organic life, "it is chaos." And for a few brief moments, at the end of this epic saga everyone across the galaxy was united against one single thing. No more chaos.

The protheans mentioned that they had built upon things left behind by other cycles. The crucible, the citadel, the mass relays. But their galaxy was still in chaos and they were eventually exterminated. They didnt have a "shepard" to rally them and essentially atone for the sins. So the question is, now that this cycle is over, what did they leave behind?...

Shepard and the galaxy left their story for the next cycle. The story of him doing the seemingly impossible of uniting them. To stop all the nonsense of playing god and living lives full of sin and hatred. If Shepard wasn't there to unite them, they would've all retreated to their own worlds. Their own selfish bubble. EDI mentions this in a conversation aboard the Normandy. She says that its confusing to her why prisoners of the Reapers would rather die than give useful information to them. In other words, she would normally "rat someone out" to survive rather than stand together and face death. She then "rewrites" her protocols to override her own self-preservation attitude. EDI and Legion both say that Shepard is the reason they think more like organics. That even a machine could learn the good qualities of being human from one man is just one of the great stories left behind by Shepard. In the end he resolved the issues of the galaxy, and all he needed was a catalyst.