The fact that Bioware made the choice to introduce the synthetic vs organic conflict and make it centralized to the entire Reaper mythos.
Okay. You really don't see difference between:
a) character IN THE SETTING SAYS x
there is x in the setting
c) developer/writer/director SAYS "I want to introduce x into the setting".
Just because CHARACTER SAYS SOMETHING, it doesn' mean IT IS IN THE SETTING. Just because DEVELOPER SAYS THEY WANTED TO INTRODUCE SOMETHING, it doesn't mean IT IS IN THE SETTING. Just because SOMETHING IS IN THE SETTING, it doesn't mean CHARACTER SAYS IT IS IN THE SETTING.
So, protip:
JUST BECAUSE CATALYST SAYS THERE IS UNAVOIDABLE CONFLICT, IT DOESN'T MEAN THERE IS ONE - just like Voldemort in Harry Potter books' talking about "love has no power" doesn't mean it is true.
JUST BECAUSE DEVELOPERS WANTED TO INTRODUCE SOMETHING, IT DOESN'T MEAN THEY SUCCEEDED - just like Adam Sandler's INTENTION of making "Pixels" funny DOESN'T MAKE THEM FUNNY.
Okay? 
ME1 and 2 we know what, when, where but we don't know who or why to their actions. They even bring up the fact on Thessia even Protheans see the repeat patterns of development. Each time the harvest happens the same set ups follow time and time again. They only remove species that have advanced to a certain point. They don't seed planets with life forms they don't harvest everyone. Yet the pattern continues to repeat it self time and time again.
Read what I wrote about phlogiston, because clearly you didn't.
As for the Protheans - you said yourself they can be wrong, right?
Catalyst is much proof of unavoidable conflict as the fact that we humans are armed to the teeth to levels ridiculously beyond anything needed to defend ourselves from nature. Why do any nation, state or tiny providence on this planet have some form of standing army? Why do the more developed nations have and continue to develop and advance weapons that are capable of destruction on such a massive scale you could almost call it divine retribution. But more importantly why does even a single solitary gun outside of hunting exist in the ME universe? Why was the Destiny Ascension even created in the first place? Why did TIM ever create Cerberus? Why does the Salarian STG even exist? Why do the Turians maintain the largest standing army in the galaxy? Why has it become a stereotype that Asari are always either strippers or guns for hire when they are in their maiden years?
You're just talking about things that have nothing to do with topic and pretend they somehow prove your point. Yeah! How did Tyson Fury won with Vladimir Klitschko, if there is no organics vs synthetics conflict?! How did Geralt fell in love with Yennefer, if there is no organics vs synthetics conflict, huh?!
Thane even has a little unquie dialoge in ME 2 if you talk to the VI on Zakera Ward. While talking to Avina on level 26 of the Zakera Ward on the Citadel, Shepard may ask how the problem of poverty on the ward can be solved. Avina will state that, according to asari futurists, poverty cannot be eliminated without Cornucopia technology, which Thane refutes by saying, "Technology cannot cure greed."
As above.
No conflict with the Geth started when the Quarians instigated a war with them that lead to their near extinction as well as turning them into the pariahs of the galaxy. Turning them into gyps stereotype but in space. This caused anger and resentment for the Quarians all directed at the Geth. With or without Reaper intervention the Quarians would have taken on the Geth again in an attempt to retake their home world. It was only a matter of time. Geth already chose isolation and enforced it by killing any ship that gets into their range. They only spared the Quarians because they were unsure of the repercussion of wiping out an entire race. How ever another completely unprovoked attack by the Quarians would alter that idea very quickly. Remember there are 2 Geth you can interact with in ME3. The Organic friendly Geth if Legion survived ME2. And the suspicious, paranoid and pretty sure Organics will screw them over Geth if Legion is never activated or dies in ME2. Guess which Geth would exist if the Reapers never existed. It isn't the friendly one you get thanks to Legion.
Yeah, because crusader kings still try to retake Holy Jerusalem... Oh, wait.
Yeah, because Native Americans still wage wars against "pale faces" to retake their land... Oh, wait.
Yeah, because pope still struggles to have power over secular governments in the christian world... Oh, wait.
Yeah, because Mexico still tries to get Texax back... Oh, wait.
Another protip: just because something happened, it doesn't mean it will happen again and again. There is NO REASON for next admiral to say "screw, let get us some nice new world, away from geth".
Yes class struggle is real. There are many examples of workers going on strike over working conditions and things turning violent to the point the police or some of their military force is called into restore order. The US has plenty of examples of this happening in it's history. As well as a continuing history of companies and corporations treating workers with the bare minimum care needed by law. And firing people at the drop of a hat if they so much as disagree with someone high enough on the totem pole. Because they can create bullshit reasons and you have no way to use any proof against it. He said she said and they can afford the lawyer fees. Because you know people that don't make more then 20K a year don't exactly have a lot of surplus money laying around.
Once again, you are unprecise and sloppy with terms. No, sorry, class struggle isn't real - because it's not a FACT, but INTERPRETATION. You can call, for an instance, Great French Revolution "class struggle" - or "uprising against holy order of things", or hegelian "zeistgeist", if you will. It's part of system of belief you use to interpret what you cognize.
Sovereign shows a high degree of arrogance but I would expect that considering what it is.
You've got to be kidding me. HE CLEARLY CONTRADITCS THE CATALYST. HE. CLEARLY. CONTRADICTS. THE CATALYST. He is LYING, or he is MISTAKEN. Tertium non datur.
Sovereign shows a high degree of arrogance but I would expect that considering what it is. The no beginning and no ends fits with that arrogant statement because it has existed for so long that beginning has no meaning anymore. And because it's body is near indestructible it will under normal circumstances exist until the death of the universe. It is an impossibility for people to comprehend that their deaths are needed.
What the hell? You think people here are morons? "No beginning no end" is fitting, because "beginning has no meaning anymore"? What kind of pathetic, ridiculous, sloppy sophistry is that? IT IS A LIE.
And how can it's body be "near indestructible", since mission in ME2 when we meet Legion takes place on DERELICT REAPER? What, Sovereing doesn't know about it as well?
And remark of "people cannot comprehend that their death are needed" is so insultingly stupid I won't even respond. Yeah! Because frickin' Boromir had no idea that his death is needed to save hobbits, right?! Soldiers HAVE NO IDEA that there may be need for them to sacrifice!
God.
The Protheans would have inadvertently created something else as well.
Sure thing, oh mighty prophet.
So you pull outside facts and ideology to defend your point about conflict not being an inevitability. But now you jump both feet into what the game says with the last point. Can you please pick a side and stick with it. Because first you are against the Reapers and Catalyst claiming conflict is inevitable but then you are fully with them claiming the Citadel and Mass Relays. They can not be wrong about one statement yet 100% correct about another statement. When both are 100% reliant on the ideology that history repeats it self.
I know it's cool and fun to bark some accusation with no context, but until you quote me "pulling outside facts and ideology" I won't bother. And how in the hell civilisations developing the way Reapers desire proves Synthetics vs Organics conflict?