@Aenemic I feel like I have already responded to the rest. The Star-Child is ridiculous anyhow, and I feel Organics vs Synthetics being singled is weird considering the indoctrinated Rachni and the Krogans tried to conquer the galaxy while the Geth just wanted to be alone building their Dyson Sphere. You ask me what I would have done differently? Wall of text incoming. Here goes.
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What would I have done different? Roughly similar. However, the Catalyst is found at the Cerberus HQ; it's an ancient VI, that speaks Prothean but is far older, gotta make the Cypher count somehow. Back on the Normandy, it reveals the possibilties in advance; the Crucible must interact with the Citadel to send its signal. Then there are different settings presented; Shepard can keep it to himself or hsare it with the crew for ideas.
Oh, and Javik the Prothean is not DLC, and in the place you find him is found a way to deactivate the Reaper's control of the Relays via the Citadel. They can still seize it, just not close/open Relays at will once they do. This is to (clumsily, I admit) plug the plot hole of why the hell do the Reapers allow the allied fleet to engage them when they can just cut the Charon relay.
Then, everything goes like into the game, right up to the scene with the Illusive Man and Anderson. But no fucking beam of divine light saves Shepard; he approaches the consoles, loads the VI, and must make his final choice. However, the Reapers are already bearing down on the Citadel to stop him, and the Crucible must power up before firing; the EMS calculates how much time Shepard has, and thus determines the ending;
-Annihilation: the Destroy ending from the game. Reapers are destroyed, but the Relays, Citadel and AIs are too since the Crucible does not have the time to target the Reapers specifically. This is done by quickly overloading the Crucible, and so is available at any EMS. Bad ending.
-Destroy : Send a signal destroying the Reapers. However, said destruction overcharges their core, and they create a massive blast upon dying. All of them. This also destroys the Citadel via chain reaction, dooming Earth and killing Shepard no matter what. Futhermore, at low EMS, the Reapers are in the thick of the Allied fleet, which suffers massive losses as well, killing most of their leadership. The Normandy is caught in the blast, killing all aboard. High EMS means the Reapers were kept at bay, and the fleet is relatively unharmed. Mass Relays stay intact, the Reapers are utterly annihilated and the galaxy is instantly free of the cycle... but what cost. Shepard dead. Earth purged of life. Several other big worlds that still had Reapers on them are also heavily damaged. But the galaxy at large survives. However, at low EMS rebuilding takes a lot of time, since with the Council dead via CItadel invasion military leaders kept the races on track. This creates a bit of an anarchic period, and in the end humanity is weakened, albeit still an essential part of the galactic community. The anti-Illusive Man ending.
-Weaken: Sends a weaker, finely tuned signal, that doesn't destroy the Reapers, but severely weakens them, cuts off their communications, srambles their targeting system, and lowers their barriers. They can now be beaten conventionally, and do not overcharge their cores upon death. The signal is not reversible. At low EMS, however, Harbinger is near the Citadel already, and has Shepard in its sights. Shepard stands defiant as Harbinger kills him minutes before being destroyed itself. Then commences a slow purge of the galaxy; the mop-up lasts many yeays, and causes much damage; at low EMS, even more than the Destroy ending. However, at high EMS, the fleets, that had only kept the Reapers at bay, not bear down upon them, inflicting heavey casualties on the now disorganized Reapers. Shepard stands triumphant as Harbinger is blasted and destroyed. The mop-up still takes a long time, and much devastation is caused by stray Reapers, but the cycle ends in a bittersweet victory. The Citadel, Shepard Earth and the Relays survive, but the damage elsewhere is graver than in the Destroy ending; in particular, many outlying colonies are consumed by lone Reapers before they are overtaken by the fleets, while Destroy mainly affects the central worlds.
Control: A new setting grafted by the Illusive Man on the VI while it was at Cerberus HQ. Only available if the Collector Base was kept. This setting is imperfect, and rather than controlling the Reapers fully it will only cause them to retreat in Dark Space and leave organics Forever Alone. That said, it takes a lot of time to charge; at low EMS, the Reapers break through before it does, destroying the Crucible and perpetuating the Cycle. Worst ending. At very high EMS, the signal fires, and the Reapers retreat without further fighting. Victory!... Except the gaame makes it clear they are still out there. In a way, best ending. If you think so.
Parley: same as any above ending (or maybe only available at Weaken), but Shepard warns Harbinger about it (who would taunt Shepard all endgame long), tell him that if the Reapers do not retreat, he will fire the Crucible and end them. At low EMS, Shepard wastes too much time, Hardinger breaks through and blasts him, worst ending as shown above. At high EMS, Harbinger doesn't buy it, and attacks; Destroy and Control proceed as planned. If Weaken is fired at high EMS, the Reapers see Shepard means business. However, if EMS is not that very high (as in, almost 100% playthrough high), the battle resumes. If EMS IS extremely high, the fleest are imposing enough to intimidate the Reapers. Shepard can then choose to convince them that he can unleash a second blast that destroys them. Defeated and weakened, the Reapers retreat into Dark Space. Like in the Control ending, they are still out there, and have all their own free will. That said, the races of the galaxy are evolving. Still, this ending will reek of uncertainty.
And there you have it. My own endings, chosen with the critera of fitting the series's theme; victory comes at a price, the right of species to exist (even the Reapers, if so Shepard chooses) and free will. While I have my own preference, it seems to me that all the options save Annihilation are palatable. I also wanted to make EMS relevant, rather than an afterthought, and makes previous big choices (Collector Base) matter.
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Edited for clarity.
