It makes perfect sense. The reapers, even in the first one, are harvesting advanced civilizations--not all organic life, just advanced civilizations. Sure, it is changed, but no more than the Darth Vader killed your father/certain point of view kind of a revelation. It is different from what they implied, but it works fine. Sovereign is an arrogant masterrace speaking to an individual that it will harvest; it speaks down and refuses to really elaborate, instead spouting rhetoric. It is a change that makes sense. Also, while they changed the ending (it was originally going to be that they were harvesting them to create reapers to fight the dark energy--god that was dumb--changed to they are harvesting them to create reapers to preserve them in a messed up twisted logic), both endings are fully encompassed in this conversation.
The collectors were a backup plan once the invasion didn't work (because the Protheans rewired the keepers and then sovereign failed) to create more reapers. The collecting was happening in the massive battle at the end of 3 (Shepard references that the citadel had been made like the collector base), and was how they originally did it, so they ARE building a reaper, and had always planned on it.
And while it does indeed seem like the idea had been resolved: you can make peace with the Geth, that is a very shallow resolution. After thousands of years of war (well, mostly a cold one), under the threat of an invasion on the magnitude to DESTROY ALL LIFE, the Quarians and Geth decided to work together. That is no real promise of peace, and the history of warfare suggests that after they finish fighting off the bigger badguy, they'll soon go back to killing each other. Is it a lingering problem that the stupidstarchild doesn't address this as an inconsequential development? Yes, but the argument that a temporary peace usurps an inevitable consequence (as calculated by the star child thingy) is pretty easily overturned.
Why did Hackett order the fleet to retreat? Because the giant ass gun was firing and he told people to get the fuck away from it. Makes sense to me. What about the upcoming Leviathan DLC? Apparently not everyone was able to make agree with the program of murdering to save and were resentful about being made a reaper. It's almost like individuals sometimes disagree with the government (here the gov. being the starchild supercomputer, the reapers being the individuals).
I don't think that ME is anywhere near flawless, but the ending makes perfect sense for the series.