--- Starboy doesn't say the same things he did before. They actually changed his motivations a great deal.
It's not about preserving Organics from Synthetics by killing Organics anymore. It's about not allowing there to be a state of separatism between Organics and Synthetics. Any way to bring about a state where there is no separation between Organics and Synthetics is acceptable to him now.
He says about the Reapers that his creators gave them form, he gave them... something, and they give him purpose. If his creators gave them Form, that basically means that his creators Built Them. So they must have been the first Synthetics that were in conflict with the Creators. Don't think that means WAR. That's just CONFLICT. Even disagreement would qualify.
Starboy says that "Everything I tried eventually failed." He tried other things, and his creators and their creations, after a period of agreement and peace, eventually came to another impasse. And eventually, he realized "Wait a second! If I make them ONE BEING then they'll co-exist in harmony!" He says that his creators objected, but it was the only way. Only way to what? To have a perpetual relationship between Creators and Created. Then there was peace. But eventually, some other race created Synthetics and they had a disagreement, fight, war, argument, heated game of strip poker, whatever. Dammit, I'm the Starboy, and it's my job to CATALYST HARMONY BETWEEN ORGANICS AND SYNTHETICS! So he does it again. And again. And he figures that the best payoff of non-conflict time to conflict time is to set up the cycles.
Think about it the way he explains it now. Conflict between Organics and Synthetics is Chaotic. Existing in Reaper State is orderly. The Cycles are orderly. He is, TECHNICALLY, fulfilling his programming and doing it in the way that makes the most sense. To a machine that does not understand concepts of individuality and rights. He's just as flawed as the other Synthetics that he says, through Synthesis, would Fully Understand Organics.
He says that he's tried other solutions. The Reapers were the only thing that "worked" according to his original parameters.
--- He explains that he doesn't just take Organics' bodies and store it in Reaper Form. He says he stores their life, their creations, their achievements. Even the Synthetics. How does he do that? Bring it back to Brainiac, from Superman. He blew up Krypton after he contained all knowledge of Krypton and its inhabitants. Because a perfect copy of Krypton still existed. Who cares that it's just data? AI is just data too, right?
Starboy is the opposite of EDI. EDI got herself a body to better understand Organic life. Legion too, as the first individual Geth, had his own body. He formed a concensus within his own mobile platform, whereas other Geth need other Geth around, or orbital platforms, or a ship. Starboy has no body. He doesn't get what actually existing in a physical universe is. I mean, remember EDI's joke? About hardening her hair for combat, or letting it be like normal hair when she's socializing? And when it's wet she CAN'T DO A THING WITH IT??? MY GOD, she understood such a simple facet of being annoyed with long hair! She'd been a singular individual for what, a couple months when she said that?
But that's actually a facet of Starboy that lets us take options that would destroy him. He defines himself as nothing but his job. And since Shepard is a more successful version of what he tries to do with Husks and Cannibals and Marauders etc, then he views Shepard as a possibility of fulfilling his purpose permanently.
--- I really, REALLY want everyone to totally disregard Starboy's old dialogue when they think about this. Redo the conversation in the EC, and only take what he says now into consideration. If you can successfully push the old dialogue (which is now NON-CANONICAL!) out of your mind, he's much, much less terrible than he used to be.
--- That said, this still isn't a happy ending, and even having the Catalyst isn't the way that I would have done it, but it's at least acceptable.