I still think they should have stuck with something less complicated. I have noticed that in many scifi recently, especially after the 90's the writers started to go over the top with complicated plots, ideas that are highly complex, setups that involve all kinds of little moving parts that are supposed to coalesce at the end. But they rarely make it. Not a lot of people can bring out the complex and make it appear natural. Most scifi like that feels forced, feels like there is just a few things too many.
I think they tried something like that in ME3 and earlier in ME2 with the whole dark energy plot, I think they tried jumping higher than they actually could, something that seemed so different, so smart for them at a time but they could not bring the whole thing to a good end. I believe the whole thing about reapers reaping the sentient organic species so that they are never exterminated by synthetic ones had potential, but more exposition wouldn't hurt, and instead of making the starbrat, they could have let the Reapers be their own controllers, Reapers doing that because they actually believe that that is the only way. All the species that were joined through the cycles also believing that the only way to live on through everything the galaxy can throw at you is to become a Reaper, a sentient semi-organic construct filled with the minds of millions and millions of each species. Instead of some sad little puppets they could have been the real boogeyman, the worst kind, the one that has the faith in itself that whatever it does, whatever the cost it is worth it in the long run. The ultimate Renegade if you will.
And the whole leviathan subplot could have gone better as well, for example the first reapers were indeed created by leviathans but instead of an AI to combat the synthetics it was created willingly out of their own people(giant space squid people but still) to combat another species that threatened them, possibly a synthetic remnant of the species that created it. So when they defeated the enemy they were created they unable to die lived on for millions of years watching other species get exterminated either by their own hand through synthetics, through natural phenomena, through wars with other species(like rachni) and decided that life is precious but preservation of a species is more important in the long run. So they went around harvesting, eventually perfecting the method to what we know.
Its still far from perfect but this way at least this way this doesnt seem like some kind of programming error in the AI( I am not sure that starbrat is even an actual AI, it might be just a very advanced VI) it would be a sentient, informed choice where the Reapers, more powerful than any single thing in the galaxy simply decided that they know better than anyone else. That they are doing it for the greater good. Also the last battle could have involved fighting a human reaper, surely they could have enough people harvested in the time it took Shepard to assemble enough support to strike back. With Illusive Man agreeing to become the controlling mind of the Reaper, for advancement and preservation of humanity. And that is how the reapers do it, harvest millions sure, but one mind, one mind willing to go to any lengths being like the morality imprint on the rest.
And the multiple choices would be to..
A)Destroy reapers, but loose all the tens of thousands of species that make them up, basically making the assertion that life in its current form, chaotic and unpredictable is better than the practical immortality of the unchanging Reapers. Shepard lives if EMS is high enough
B)control the reapers, slaving them to a control of Shepard's uploaded mind if EMS is low or to the control of the crucible AI, if its high, forcing them to adhere to a set of rules, stopping the cycle but preserving the Reaperized species. Making them into the galaxy's biggest work gang. (leaves the possibility of Reapers leaving permanently to dark space or something like that)
C)Synthesis(not really), unchaining the millions of minds inside each reaper from the control of the main one, giving them all the option to see the horror they have done, Shepard sacrifices himself as a virus is uploaded requiring the organic mind(Shepard's) and the synthetic mind of Vendetta basically making Reapers into kind of like geth with millions of individual minds gaining consensus on their actions. Reapers fight with each other, some simply leave, others leave caches of technology before committing suicide or leaving. The reapers could still be around but they are not such a threat anymore, their remnants defeated by the combined fleets and forces.
This way they could still have reapers, still have multiple ending choices and yet without the whole plot block that they found themselves in.