End of the day the Catalyst's explanation for the Reaper's existence is the most obvious dumbass circular logic I've seen in quite a while. Organics will be wiped out by synthetics, so I've created synthetics that wipe out advanced organic life every 50k years in order to stop them from being wiped out by synthetics...? Anyone with half a brain has to look at that sentence and just marvel at the stupidity.
Plus, no matter which ending you choose the Relays and the Citadel are destroyed. In ME2 Arrival DLC, we see first-hand what the result is from a Relay being destroyed. Basically a huge part of the Batarian Hegemony (The guys with four eyes and wrinkly heads) is wiped out because of the destroyed relay basically going supernova when it's disrupted. In the ending you can see the shockwave from the Crucible spreading to the first relay and destroying it. Then you see the galaxy-wide spread of said shockwave, and massive detonations spreading to every relay. Now, knowing that a relay going boom has the destructive power to destroy an entire starsystem: Until Bioware says differently it's fair to assume pretty much the entire galaxy is bombed back to the stone age no matter which ending you choose. Continuing down this train of thought: You can liberate the Quarian homeworld, cure the genophage, give the Geth free will amongst many other choices. Yet at the end, every single fleet in the galaxy is gathered in the Sol system (aka. in the vicinity of Earth), and with the relays' destruction they have no way to get back to their homeworlds. The Quarians' homeworld, for example, is across the ENTIRE galaxy. On top of that, Turians and Quarians can't eat human food either due to their different biology, and Krogans (now that the Genophage is cured) will pretty much breed like wildfire. What was the point of giving all these different species their collective lives back in one form or another, if the ending is just going to piss all over everything you've done?
ON TOP OF THAT (Yes, as a longtime fan I've given this way too much thought) the three choices are completely pointless.
1. Kill Shepard, control Reapers, destroy relays.
2. Kill Shepard, create new DNA in form of symbiosis, destroy relays, Reapers leave
3. Kill Reapers, destroy relays.
I'm just going to ignore the second option, because the notion of the entire galaxy somehow becoming synth-bio hybrids feels like such a departure from the rest of the games so far, like Baker said "from Star Trek to Star Wars". Suddenly there's this magical force capable of metamorphing the entire galaxy. Yeah no. On the other choices: basically this AI-God-Child-Thing is completely willing to give up control of the Reapers, or indeed have Shepard kill him/it and all the Reapers - because Shepard showing up is proof that the current solution doesn't work anymore? Why doesn't it simply call off the Reapers then? How about the Geth and the Quarians making peace? The Catalyst says the solution is there because synthetics will always turn on their masters and kill them. In this extinction cycle those synthetics are the Geth. Before ME1, the Geth attack in self-defence and drive the Quarians away - but allow them to retreat as soon as they're no longer a threat. A splinter group of Geth then attack Eden Prime and other organic-settled worlds UNDER ORDERS FROM THE REAPERS. In the second game the Collectors (half organic-half synthetic) attack human settlements UNDER ORDERS FROM THE REAPERS. By ME3, the Geth are fighting a war with the Quarians simply to DEFEND THEMSELVES, and then get CONTROLLED BY THE REAPERS ONCE AGAIN. When they are freed from the Reaper signal, they simply want to make peace and live their own "lives". If Reapers are here to somehow protect organic life from being wiped out by synthetics - why are they the only synthetic race that continuously attacks organics? Circular logic. We don't want you getting wiped out by synthetics, so we made an army of synthetics to wipe you out.
And heck, in the first game it's said that Sovereign was left behind to ensure the Reapers could come back through the Citadel and kickstart the extinction. If the Catalyst - the thing that controls all the Reapers, has always lived on the Citadel, what was Sovereign's function? Why didn't the Catalyst just activate the Citadel when he wanted the Reapers to show up? Sovereign, the primary antagonist of the first game, becomes completely irrelevant. It's simply a dumb plothole that can't be plugged with any information we currently have.
As a final note, the original ending written by Drew Karpyshyn (the original lead writer during ME1 and ME2) is foreshadowed through the entire series. But Drew has left Bioware, and apparently his ending wasn't good enough or something - even though, as mentioned, the foreshadowing and the work up toward his ending is still very much there. This is basically why the ending feels like such a mess. The Catalyst-AI has never been mentioned before, and only exists in the story for those last five minutes. Hell, the old better ending possibilities are still readable in the .xml files that were leaked pre-release!
And even if I was to accept all this plothole-riddled bullshit as the ending; it's still not a fitting ending to a series that has prided itself on player choice and character building. There is no closure, no catharsis. In short the player doesn't have a fucking clue what happens after the ending, or if any of Shepard's choices during the three games matter at all.
