Beyond the flawed logic of the Catalyst, why was this never explained?

No the problem is they decided to go a completely different path in ME 2. Thus preventing the game and story from advancing in a logical path.  The entire basis of ME 2 plays out like it is trying to be the first game in a trilogy.  You don't start off by showing off the ultimate bad guy of the trilogy then downgrade from there. You start off with Collectors then upgrade to Sovereign then upgrade to Reaper invasion.

Not that much went haywire. And while there is a lot of improvements they could make a large portion of the problem and flack it gets is from the minds of players. Which is completely subjective rather then any objective problems.

ME:A could be a great trilogy the problem is they are attempting to create it while trying to completely bypass ME3. Which creates a whole mess of new problems. And weakens the over all set up preventing any possibility of a trilogy happening. Because what would be the ultimate end point? Establishing a colony and contacting the Milky way? That would require addressing ME 3. Which they are being pussies about.

I think the idea here is to say that at some point, we don't know when but we know that in time it will happen, some AI lifeform or species will evolve so far past organics that we become meaningless to them like ants are to humans, making them eradicate organics for being disposable and hindering life completely, and ironically reminiscent of the Reapers' relationships to the harvested species. The problem with this however is that the Reapers are invalid as the problem in this scenario because they're preserving life not committing total genocide, and the other problem is that this entire notion is so far beyond the scope of Mass Effect 1, Mass Effect 2 and even Mass Effect 3's plot it's an entirely different story, and that is why the catalyst scene falls flat. Without Shepard to question him and use Ethos to inform the audience about how wrong it is or what it means to be organic or being forced to pick a choice, to resound the themes that have been going throughout the game, prevailing as a united galaxy and righting the wrongs and sacrificing ourselves for the horrors (genophage and Rannoch, stopping Cerberus etc.), the final conversation doesn't do anything to conclude the plot. The point is exactly what you think it is, that there's this issue that exists past the scope of the narrative it exists in and you just can't relate to it as being the central issue that is the cause for literally everything in the trilogy at its root. The story ends on a logical fallacy. Like OP says, there are no presented variables or points of refute and no dissection of such a giant issue, only a brief exposition and Leviathan DLC to back it up.

It ended this way because Casey couldn't see how faulty it was, Mac is not intelligent and the remainder of the writing staff didn't take issue with it unless they did and Casey went "artistic integrity" and refused to let them change it when they began making handwave DLCs and extended the original ending. More importantly they didn't bother to even listen to the constructive critics out there (aside from the whiny, bitchy ones), when there were so many pointing out exactly what the real problem was, but BioWare couldn't see it, and unless it's PR they still don't see it whenever they talk about it publically.

There's also something called "digression" and you could use it right about now. I could too tbh. I think we have made each our take about what OP asked about anyway and our argument has gone on way longer than necessary and we just had pretty much the same discussion in two other threads IIRC.

For BSG, the synth side, ie: the cylons started doubting their purpose once the organic hybrids started having 2nd thoughts due to interactions with regular humans.The plan to destroy the last parts of humanity that is. For ME side, perhaps something similar was embedded into Legion? To basically find out if the organics could be useful or to try to understand. Not that the ME synths doubted much. It was more like they wanted to see what kind of variables would be needed to co-exist or avoid humanity/other species all together.

The organic side of the equation might have to put collective differences aside for a greater goal, IE: trust the synths some more, but thats hard for them to do because of individual drives. In BSG you seem them try to work with the cylons but its a tense situation/alliance at the best of times. In ME land, so far, other then EDI or even some avatars for the Geth, humanity and everyone else hasnt had too many great experiences. Its another conundrum to work through. I cant even remember if I got the Quarians and Geth to work together in any of my ME3 saves.

If it's meant to hold up having the 3 possible outcomes is effectively the message of the story. Otherwise why do we willingly go along with his proposal without a single question to his arguments?

If it isn't meant to hold up then why aren't we having an ideological debate that resound the themes that argue against it such as the conflict on Rannoch, galactic stability, throwing evidence against it, plus points for Wrex and Eve and a cured Genophage, minus points for Wreav without Eve, or one side of the Rannoch conflict falling? Why aren't we using logical problem solving to dissect why and how the Catalyst's thinking is flawed, but instead just go with it?

Such a tremendously missed opportunity.

No one had ever actually completed the Crucible so no one knew of any possibilities.  OTOH, the Catalyst implied (I think) that one cycle had come close but not been to choose Synthesis.  Perhaps that person or people chose Refusal and the cycle continued.  I even sort of remember that maybe Shepard is also a product of the cycles and a similar person may have arisen in the past.  Can't say where that idea came from though.

I suspect you're right that the Catalyst couldn't be convinced.  It could only understand its own logic and to us that logic is nonsense.  Shepard should have suggested that the Reapers themselves be harvested into a mega-Reaper that can protect the galaxy from war.  Then the Reapers are defeated and Mega Reaper intervenes only when synthetics and organics are on the brink of annihilating one another. 

Dunno. By design I think it made for a bad final scene.

It seems to me like the recurring theme is slave rebellion.

We constantly strive to create faster, smarter technology in order to make our lives easier but when this technology becomes too much for us to handle then what? Do we give up on advancement? No of course not.

So we will inevitably continue to make ever more powerful technology and we will inevitably usher in our own destruction as our slaves inevitably rebel against their masters.

Or maybe some form of compromise can be reached. Maybe even coexistence. But what form would these take? Of what use would we be to them? What could we do that they couldn't also do but better? They have no need of us whatsoever and they would surpass us so very quickly. We would become little more than zoo animals. Squirrels in a park. Something to throw crumbs at and then put out of your mind.

Well, sure, but where'does admitting that get us?

People who say that generally have the least convincing argument to back up their stance.

Why so surprised?  For example, I only just started playing ME games about a year ago.  I missed out on the discussions that took place in 2012.  Continuous influx of players means discussing some of the same stuff again.

No. No you do not.

And they never pretend to be your friend. The argument was that the actions of the Reapers couldn't hold up to scrutiny about it being the most effective or justifiable action.  It is the most effective method. And it is rather justifiable if you take the long view rather then short view.

But at no point do the Reapers or I pretend or claim to be friends.  Catalyst wants a problem solved and I want them to stop killing us so mutually beneficial agreement that benefits both sides.