I don't think that's really the case. Yes, there are organics and they fight synthetics but I don't think that's thematically what the conflict is about. Zombie stories aren't thematically about people vs zombies even thought that's a recurring conflict, the zombies usually represent something else like consumerism, self destructive nature, human hubris, etc. Synthetics in the ME series increasingly became stand ins for racial issues. They were just another rubber headed alien... only with metal instead of rubber. Furthermore, anything that could be gleamed was concluded with Rannoch.
To clarify, I don't mean the main theme of the series was synthetic vs organic... though the reapers are synthetic... and the entire plot revolves around us trying to stop them from ending us... hm.
Anyway, my point was that there are aspects of synthetic vs organic throughout the trilogy. There is MORE to it then just conflict, yes, but conflict itself is a reoccurring theme. Zombie movies have a theme of having zombies in them, with humans trying to survive against said zombies. There may be a deeper meaning where they're representative of something else and thats fine, but they're still zombie movies.
For example look at the Walking Dead game series. The majority of that game, the main theme, I would argue isn't actually about the zombies. Its about the group of people trying to survive together with zombies just being in the background. The games focus is more on the characters surviving then it is the actual zombies, imo. That probably has something to do with why I loved the series so much even though I'm not really a fan of zombies.
However, no matter how prevalent other themes or nuances are present in the series you can't deny that zombies are a theme, regardless of what else they may or may not represent on a metaphorical level. Synthetic vs organic in Mass Effect has been a theme present in each title. You can go through the entire trilogy and find instances where this is the case. The main story of the first game revolves almost entirely around this conflict as the main enemy force is the geth.
You can argue that collaboration and peace is a theme as well because you have all these races coming together putting aside their differences to work together, even the geth later on. However that doesn't change the fact that the conflict is present in all of them. I'm not saying this is the only theme but it IS a theme. Hence why I don't think its fair for people to act like it is something only brought up in the ending - because it isn't.
As for Rannoch resolving the issue, I say nay. Billions of years of observing organics has concluded that there exists a pattern of conflict. Shepard potentially brokering a peace with the quarians and the geth (which up until the ending has only lasted what, weeks?). In the Mass Effect universe, which is fictional mind you, this pattern exists. It exists because beings that have existed and observed the cycles of billions of years have observed it to be so. This billion+ year old perspective is not made invalid just because the geth are playing nice for an astonishing few weeks.
I will say that synthetic vs organic being a reoccurring pattern in the galaxy is something only ME3 brought up (though not at the end) but regardless the synthetic vs organic bit itself, even if only in our cycle, has been present in the trilogy since day one.
The end was dealing with an issue that the story had no where near enough depth or intelligence to support. This is really evident when you look at the Catalyst's language. It uses such vague and generic vocabulary that you can use it's argument to talk about almost any kind of conflict you want. I find it telling that no where in the ending sequence we can talk about the past experiences in dealing with synthetics.
The Leviathan dlc clarifies some of it. Frankly I think the Leviathan dlc was made specifically to give credibility to the ending. Not very satisfied with it, personally, but there it is. Personally I think the ending, at least in its current form, would be the WORSE time to go over such details. The fact that Shepard talks to the starbrat as much as he does is pretty staggering, giving the gravity of the situation. Every moment you waste bickering with the kid how many people die right outside? Our fleets will not last forever, they're giving their all to protect the crucible at all costs. While they're giving their lives to ensure the crucible isn't destroyed you're standing up there wanting to give a lecture to the master of reapers.
This is a horrible, HORRIBLE time for a history lesson. We know the catalyst has tried other solutions, we know the reapers isn't its ONLY solution only that its the most successful. Any solution we can think of "oh have you tried so-and-so" we should assume its tried. Its billions of years old and has been doing this far longer then us. I find it naive that any organic, other than perhaps Leviathans, could claim to have a better idea that the starbrat hasn't already tried and found it to be lacking.
We do talk about its past experiences in dealing with synthetics in the ending, its just vague about it. Which makes sense, given the situation. Again, this is the worse possible time to be having a history lesson. Hence the Leviathan dlc. Which didn't have as much depth as it should have, imo, but it at least does provide more substance towards the endings.
As for the solutions I understand that the Catalyst has some different perspective on preservation (although I do wonder how it got such a view when programmed by the Leviathans or why it would store everything in the relatively fragile body of a Reaper). It's the other stuff:
Lol, relative to what exactly? Relative to space ships? They're a hell of lot more durable then any organic body we could have. Not to mention ageless and essentially immortal. Though those two are perks the Leviathans share as well, which are arguably the apex of all organic life.
Like why does it offer up Destroy and Control when Synthesis is available? For Destroy it explicitly states that it isn't a solution to the O vs S conflict, it only offers it because the Crucible can enact it. Control is similar as what Shepalyst will do is an unknown. Why doesn't it explore non-Crucible options like just leaving, that's seemingly more sensible than Destroy from the Catalyst's perspective. Why can't Shepard just tell the Catalyst to order a universal self destruct sequence or fly into the sun? It's just as valid as Destroy only with less collateral damage which if anything makes it better for everyone. The only way anything the Catalyst does makes sense is if by 'change the variables' the Crucible rewrote part of the Catalyst's code in such a way that it had to use the Crucible and only the Crucible (which doesn't make much sense either).
Good questions. Though, honestly, imo, you should back this questions up a few steps. Instead of asking why it offers such and such instead of synthesis why not ask why it offers anything at all. The catalyst is the one that activated the elevator that took Shepard up there. It is the one who woke him up. It is the one that presented the choices. Why do any of that, period? Why not just leave him down there beside Anderson, passed out and bleeding out?
These are just further examples, imo, of why the catalyst is such a flawed execution. These things you mention are REAL criticism that should be used against the ending - not the kind of crap people make up and pretend are problems even though they're not (yo dawg). You can headcanon answers to these questions but none of this fixes the real problem which is the catalyst itself.
Frankly, I'm less bothered by these types of questions and more bothered by the fact that it even exists. If we remove the catalyst we wouldn't have these problems in the first place. Asking these questions to be resolved implies that if there were answers of these questions the catalyst would suddenly make sense in the lore. I don't believe it would. Its existence is a plothole to me. Adding to it won't fix that - the only thing that can fix it is if they rewrote it and changed it into something else.
Why is the Catalyst even letting Shepard choose anyway? The common defense I hear is that the organics proved something but that isn't the case. The Catalyst still believes that the O vs S conflict is alive and will still inevitably end the same way (the only reason Shepard is up there is because the Catalyst made some simple mistakes, next time just turn off the beam). The Reaper solution is still better than Control and Destroy, and still seems to work just as fine as it did before (species are preserved and organic life goes on). If the Catalyst didn't want the Crucible to be used it could have left Shepard down the elevator or if the elevator came up on it's own free will just not talk to him (I doubt Shepard would just start shooting tubes or get anywhere near surging energy). It really diminishes that the Catalyst experimented all these eons when it's just as susceptible to SpaceJesus's aura as everyone else is.
In hindsight, I should had read your entire post instead of replying to it in chunks. 
Anyway, these are all, imo, very valid complaints and criticisms one could and indeed should have about the ending. THIS is the kind of stuff I like to see people complain about. I just hate it when people make up stuff to complain about or misrepresent the story. IMO, all the false or mislead criticism distracts from the real issues. This is why I take such offense to people using the "yo dawg" meme, just for example.
the reapers are all there is in their universe, being Apex and all... then, their own creation took that away, completely destroying that identity. Their motivation stopped from being apex to being at all. The weird part imho is that they were only just surviving by seeing the need to control the very reality that surrounded their existence. That what started out just an ideal tool, ended up being a 'better' them. A new and improved Apex race of one (catalyst) who is the boss reaper. As we know that the leviathan are the pre-racial/missing link between the catalyst alone and the catalyst cloud linked to all the races within the reaper ships. The leviathan actually exist within that reality somewhere.
In any event the reapers "motives" started out simply to harvest beings like the catalyst did the leviathan, who ended up the first of such a race. After so many cycles the catalyst/head reaper "changed" with the times and the un imaginable "Mentality" of the cloud. The Geth have an uncanny/inorganic insight as well as the machine people, who are related to the first races in the MEU.
I think I have things to say about this... but I don't know. I don't really understand most of it. Any complaint or correction I make could just me misunderstanding what you're trying to say.
This has probably already been addressed in these pages but please humour me and help me out with something. The original Mass Effect tells us that the reapers return every 50k years or so to harvest all advanced organic life in the galaxy. I read into this that they were indiscriminate, harvesting all species with the same motives. Mass Effect 2 introduces us to reaper reproduction, for lack of a better term, that Shepard is the reason why humanity were chosen to be this cycle's new reaper. This is backed up by some of Harbinger's taunts such as: "Asari: reliance upon alien species for reproduction shows genetic weakness.” and “Turian: you are considered...too primitive.”
So what happens to these species? They get "reaped", but is Harbinger saying they aren't worth preserving as a unique consciousness? Also, does this go beyond the primary purpose behind the reapers which is explained by the Catalyst? Why have they evolved this racial preference?
This is actually, I believe, explained in the codex.
* CAPITAL SHIPS are Sovereign-class Reapers two kilometers in length. They typically target the dreadnoughts, defense installations, and industrial cities of organic civilizations. Experts believe the Reapers harvest a single species of organics during each cycle of extinction to create these massive ships. Some capital ships are capable of launching small drones equivalent to fighters.
* DESTROYERS are 160 meters long and, in astounding numbers, make up the bulk of the Reaper fleet. They engage cruisers and other, smaller ships, as well as communications posts and enemy command centers. Research suggests destroyers are created from those species that are not harvested to make capital ships.
Humanity is, obviously, the one deemed suitable for becoming the new Capital reaper. The other species will be turned into Destroyer class reapers. I believe this is what Harbinger's taunts were alluding too.
Btw, Vazgen, I'm surprised you didn't bring this up. Could it be I finally remembered something you didn't?! Mwuahaha. I still have some catching up to do, but its a start. Your move.