I'd like to start by saying this thread, as I understand it, proposes an alternative method of storytelling - so what I've been addressing here is the way the writers presented the story in the main game, irrespective of DLC.
Its true that they could have been organic. You're not to first to bring that up and I still find it surprising. What does that change, honestly? It's still synthetics fighting organics. The catalyst never said that they get in conflict for one specific reason and that reason alone. It just says they get into conflict. Which they have in ever single case presented in the series. It doesn't matter what caused the conflict or who is the blame or anything of the sort. None of it changes the fact that its still synthetics in conflict with organics. It doesn't matter what side short first or if the machines could be supplemented with Alien Race B.
It matters because it is the crux of the problem the Catalyst claims to be trying to solve. "Without us to stop it, synthetics would destroy all organics."
The writers did not demonstrate the existence of that problem imho. The first rule of fiction: Show, don't tell.
Based on what the game actually shows us, I'm more concerned about the Krogan - who did chase the rachni down to a point of extinction - than any synthetic threat. Also - Batarians are running on pure hatred, and may also pose a threat.
As for synthetics posing a high threat than organics, well, imo that's self-evident. Hell almost all of the sci-fi movies that deal with this like to point out how powerful machines are. They don't sleep, they don't eat, they don't feel your pity or remorse. They can be hundreds of times stronger, more durable, and infinitely smarter than any organic. IMO the biggest stretch sci-fi does with these types of stories is that they usually suggest humanity actually have hope of beating them. They also tend to nerf the machines in strange ways just give the human forces leeway in beating them.
"Appeal to genre", might be an apt description for this argument. There are always 'stretches' in fiction - you've identified one, and I would suggest that the idea that they would ever be motivated to start a war with organics is another. As has been suggested elsewhere (by lakus, I believe), they may be perfectly content to sit in a server calculating pi for eternity. Fiction - and fictional species - are designed to create conflict.
Here's the thing: as organics, we might appreciate spending some time in, say, Hawaii - but for a synthetic, is there any difference between actually being there versus downloading and processing data about it? The Hammerhead missions sort of pointed out these differences with its comments about organics taking note of scenic vistas.
Again, I'm talking about what is presented in this story in the MEU.
Beyond that though one thing to consider is the fact that synthetic conflict is a controllable variable. Organics will fight with organics. Its inevitable, can't really be controlled. You can't keep race A from fighting with race B. However synthetics are not natural. They are created by organics. You may not be able to stop organics from killing each other but you certainly can prevent synthetics from killing organics. How? Easy. Don't make synthetics. They are not a natural phenomenon. Long as you keep from making them you don't have to worry about it. You can remove that variable from the table.
Yep.
But here's the scenario: reapers leave the relays and citadel for organics to find so their technology will evolve down the paths desired by the reapers. Reapers hide out in dark space, removing all traces of their existence between cycles. At no point do they attempt to prevent the 'problem' from occuring. It gives me the impression of an ulterior motive.
Like maybe: "Like a cleansing fire, we restore balance. New life, both organic and synthetic, can once again flourish"
The Leviathans who programmed the original intelligence did not prioritize prevention in its algorithms - that would have been too easy. It sounds like they did include some ability for self-correction, since the Catalyst mentions having tried other solutions in the past - but ultimately, the thing gets stuck on endless harvest cycles. Which makes me wonder if bringing forth a steady stream of new life forms may have been one of the goals with which it was programmed. And, hey - if you're a Leviathan, having a wider array of lifeforms to enthrall would be a good thing.
Of course, the 'intelligence' (Catalyst) may have changed over time, and is no longer what the Leviathans originally programmed.
You'd think the Leviathans could have kept their thralls from creating synthetics that would eventually cause problems without needing to create a special intelligence to solve their problem.
The geth wouldn't be hired like mercs. Geth are... it's complicated, okay? Lol.
Yeah, I remember the discussions with Tali explaining how they network and get smarter when there are more of them. Poor Shepard didn't seem to understand - lol.
Still, I don't see any reason why Saren could not have worked with any other merc group - and he did also have some Krogan mercs. He had the power of indoctrination on his side.
The majority of the geth believe they should achieve their own future and not accept the reaper's aid. They believe the journey is as important as the destination, basically. A small fraction of them however believe they should accept the reaper's offer. Neither result is an error, both are right. They accepted each others decision and the heretics were allowed to leave. They basically split based around philological differences.
Interesting, isn't it, that synthetics can so easily tolerate differences. Ahem.
Theoretically you could reprogram them. Theoretically you could reprogram organics too, though. I'm not sure one is necessarily any easier than the other. So while possible in theory the practically of it is in question, imo. The difference between the two is that with AI, unlike organics, reprogramming them might be your only hope for victory. Where as organics you can get victory over in a great many different ways.
The idea that synthetics have no exploitable weaknesses may be a bit of a stretch, at least with our current understanding.
I've always found it a bit odd that geth environments have no air, and they are presented as thriving in a vacuum. It would imply that they are impervious to changes in pressure, and don't need air - or even radiant - cooling. They also need a power source and may be affected by electromagnetic energy and other disruptions (we have disruptor ammo, after all). Their platforms may be destroyed with conventional weapons, and their organic enemies could have synthetic allies on their side.
True but the lore is lore. The story presents it as the truth. Assuming they're all lying to us is headcanon. I go with lore, myself.
This is hardly the first time the series has done this, though. Lazarus, just for example. How does that work? Just does. You could go through the entire trilogy with a fine comb and find many examples similar to this.
Don't get me started about the Lazarus Project - lol.
What I'm saying is that the Catalyst puts forth some exposition that doesn't gel with what we've been shown in-game. They're violating the "Show, don't tell" rule. It's a lot of the reason why so many players went "WTF?" when they met the Catalyst.
They're certainly arrogant. I'm also sure they do view things very differently from us lesser species. Though I don't see how any of that could actually influence their observation of the pattern. The pattern isn't exactly complicated: organics races build machines, machines turn on them and wipe them out. They never really said what the cause of it was. Just that the conflict kept happening. That's a simple enough observation that I'm not sure how it could misconstrued by perspective.
It would certainly impact their value system and judgements, and also influence the logic they built into the 'intelligence'.
I hope you had a pleasant experience throughout. It's my favorite game series. 
Thanks. If I didn't like it, I prolly wouldn't be here.
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