You make some interesting points, but I think you completely miss some other big factors.
The Citadel species were hardly perfect and completely peaceful. Twice before they faced near mass destruction at the hands of another species first with the Rachni and then the Krogan. Even then there was still an immense amount of machinations from each race that given time could easily have boiled over. Batarians were constantly trying to find a way to dominate everyone. The Krogan were hell bent on exacting revenge on the Turians and Salarians and dominating the galaxy once again. Cerberus was doing its best to have humans dominate all others. The Asari were hiding a massive Prothean beacon to ensure their own quasi-dominance and the Salarians were constantly doing shady shit to undermine other races and come up with new ways to practically obliterate their enemies.
True, but the Krogan problem was specifically due to the mucking about of the Citadel races trying to combat the Rachni for peace. And, it's been years since I've played ME1, but weren't the Rachni considered essentially intergalactic pests? In the sense that they weren't seen as an intelligent lifeform to be reasoned with?
The other points are all excellent and what frustrates me the most about the Mass Effect series. They have some amazing opportunities and examples to really bring about a good, thematic story but they constantly pass over those opportunities. If they had used any of these as a main focus to highlight the inevitable goal of the Reapers, then their ideas wouldn't seem so out of left field. But instead we get the Reapers going on about synthetic life and some bizarre adherence to the idea that synthetics will want to wipe out organics... because they just wanted to keep using the Geth as villains I assume?
As for the Citadel and Relays giving species the ability to dominate all others, this is true to an extent, but for all its advantages its highly disadvantageous because the second a species achieves space flight and finds the relays they are on the path the Reaprers planned for them, which they can capitalize on and use against them when the time comes. If not for the Citadel and Mass Relays these species would have to develop their own systems of galactic transit and technology which presents a huge issue for the Reapers to overcome and would more than likely lead to a species dominating others more likely simply because it would take a long time and a seriously powerful species to create such advanced technology.
This really diffuses a lot of the weight they were trying to put behind the Reapers in the first game. The choice of their name was very specific - they wanted the player to fear these enigmatic species. They were meant to be an incredibly ancient, unknowable and ruthless entity.
But what does this tell us of the Reapers if they're worried about some upstart race popping up and creating a device to destroy them in 50,000 years. They've seen the passage of millenniums and should have the stance that we are never going to achieve a means of opposing them because we are so insignificant.
If they were truly afraid of species creating sufficiently advanced technology, why wouldn't they just update their cycles to occur every 30,000 years?
Plus for all their unity and good intentions, the second the Reapers showed up all the races said screw you guys and went off to save themselves and their own kind. If not for Shepard the Asari, Salarians and Turians would have all died on their own attempting to save themselves and not caring about the others fate. Everything is still there more or less to support this kind of explanation for the Reapers.
I haven't played the third game, but this is one thing that made me a little humoured when I read the leaks. This was done to obviously make the player feel important but if there has ever been a precedent set in history, it is that an outside threat almost invariably drives disparate factions together in a common defence.
The races should have been pulling themselves apart before the Reapers arrived and Shepard had to pull them from the rubble to unite them instead of them fracturing at the appearance of the Reapers.
From Ashes DLC supports this whole idea even more so with everything that Javik tells you about his people and the Prothean society. They completely dominated all other species forcing them to join their society or be wiped out completely. They had numerous massive wars for control of the galaxy and were in the middle of a catastrophic war with a synthetic race when the Reapers arrived. Seeing at the Reapers have come and gone probably more than a thousand times I would wager theyve seen more instances of the Prothean society than of current Citadel coalition.
I do like how the Prothean did not meet the expectations of the modern races. This idea that they were warring with a synthetic race rubs me the wrong way. Why wouldn't there be any evidence of this villainous synthetic race laying about? It's not like their bodies were organic and would decompose. But it also confused me how no one took Shepard seriously even after they had a Reaper body to examine and realize "HOLY SHIT THIS TECHNOLOGY IS OLD."
Also, the idea of a Prothean bombing around for so long just rubs me the wrong way. I like the execution but hate the idea behind it.
When you have an ancient lovecraftian machinegod race of intelligent spaceships, when they say "My kind trascends your very understanding", that should be the clue that any attempt in the future to explain them will only be a burden.
The fact they had them as machine-gods kind of left them with a bullet in the foot in the first place. A species of machines has to be made by someone - you can't evolve a robot. This human element immediately makes them understandable on some level.
It also makes it really easy to defeat them. I mean, a single digit change in the Geth programming caused a faction to split off and reject the Reapers as their gods. It is what has always bugged me about artificial villains from this series to the Matrix and most things in between. Robots, especially ones whose creator is still kicking around, would be so easy to control and bring to heel.
