The collectors make some amount of sense, as a backup... Keep an eye on things while the other Reapers are maxing and relaxing in the intergalactic void. Though, is it even clear they're anything beyond Harbinger's pet project? Those first few thousand years of the cycle must have been pretty boring, poor dude just needed a way to keep busy. But it makes perfect sense - even ignoring the dark energy stuff, once Harbinger found out that Sovereign had bought it, it'd be damn keen on finding out why, and either making sure it wasn't a real threat to them, or neutralizing it if it were.
However - unless I missed something - that raises the other matter: Sovereign and Harbinger had absolutely no coordination. That seems like rather a missed opportunity for team reaper. Stopping just the one barely worked in ME1, the tag team would have cleaned the Council's clocks and the galaxy would have been sunk three years earlier. Just goes to show how making it up as you go along almost invariably tends to mess up earlier installments when reconsidered in light of the later ones.
Now. That ending. I mean, it was somewhat spoiled by knowing about the shitstorm going in. But I'd avoided any specific spoilers...
Starchild McSpaceghost - sure, it's the kid, and I did naturally assume it was taking a form from Shepard's memory, but that only makes one wonder why that form, instead of, say, anyone else Shepard has lost, even in just this game; sure, because children are ever so evocative of pathos, but the game was so damn belabouring of that point it was jarring - anyway. Starchild McSpaceghost says a bunch of stuff that kind of sort of explains the situation and Shepard plays the galaxy's worst ever game of three card monty, trying to guess which door has the least shitty epilogue hiding behind it.
I can sort of understand where it's coming from. It fears the creation of some sort of synthetic life that will destroy organic life. To forestall that, it prevents, via Reaper liquification, organic life from reaching a point where it will create such a synthetic life, by incorporating and somehow preserving some of their essence while nonetheless removing them from the galactic picture. Less advanced species keep on trucking until the next cycle.
But why should it believe that to be inevitable? If we presuppose the original creators of the Citadel and/or the Reapers and/or the Relays were themselves organic (seems reasonable enough) then such a thing has obviously never happened in their experience - or they wouldn't be around to worry about it. Perhaps it was threatened - but it didn't happen. Just as it didn't happen to the Protheans, and didn't happen with the Geth. Conflict, yes, but annihilation (kill, not just all humans, but all organic life!) doesn't (and obviously didn't) happen.
Why, furthermore, should it assume only organic life is capable of wiping out all other organic life? What if someone wants to blow up some stars? Tailor one mean-ass virus (like in ME2, but it kills everything). Plain ol' warmongering (tweak the breaks and the Krogan might've been able to, the Rachni might've been able to, hell, the Yahg might've been able to, and that's just the latest cycle). This has some sideways logic in that the harvesting prevents nova devices proliferating into the hands of small enough groups with big enough grudges, but this isn't anywhere mentioned as part of the justification.
There is an out to this - the Crucible. Which has been passed down for who knows how long, and has been blithely built by the current races with little idea of what it actually does, let alone how. Hell, maybe the initial preliminary design was planted along with the first cycle, and the plan all along was for a slow accumulation to finally force a change of methods when enough time had passed and the galaxy as a whole had progressed far enough by cumulative design (now THERE'S a Xanatos gambit!). But in any case we literally have no idea what Starchild was like before we stuck the Crucible (aka "that Forerunner science thing we don't know what it does") to the Citadel (aka "that other Forerunner science thing we don't know what it does"). It says it changed him, and supposing we take its word, we don't know how. If only we could ask the damn kid a few questions.
What the choices actually are, and actually entail, well - that's a problem. It just doesn't fit together. And that's sad, since apparently we're stuck with it.
It'd've bothered me more, only just a few days prior I got around to watching the last episode of The Prisoner, after managing about one a week for the last... 17-plus-a-few-extra weeks, I suppose. Now THAT was an ending. Dem bones, dem bones, dem dry bones...