*Warning: Off-Topic rant inbound*
Well ultimately that ties back to one of the things I disliked as the trilogy moved on, the 'humanization' of the setting. At the end of the day the Krogan, Turians, Quarians, etc. were humans with rubber suits on. ,snip>
/rant
Well, ... What did you expect?
As far as we (currently, and leaving aside personal beliefs) know, we are the only intelligent species in the galaxy. We can only use "human" behaviouer and history as a guide. For instance science will anthropomorphize the behavior of an Ant Colony, because we have know other way of describing how a Queen Ant and the colony at large "think".
How de we "know" that an Ant colony, given enough time, might not evolve into something more? Something like the Rachni? We don't. So all we can do is speculate on what we see, and can study and make (barely educated) guesses, and that's for another "terrestrial" species. Even amongst our own species, we can sometimes barely fathom the way certain "cultures" view the world, and enact various behaviors, some customs almost seem "alien" from one culture to the next.
So how on earth (no pun intended) do you expect a game developer to make an "alien" species feel alien? The only way they can. By looking at "human" cultures both past and present, and by looking at "science" past, present and future, and using that wonderful thing called "poetic license".
They "alienify" (I just made up a word
) various "human" religions, cults, histories, behaviors and cultures. because there really isn't any other way they can tell a story, and have us, the players, understand and relate to that story.
... ...
As for the Reapers, I think you are overlooking one of the central themes in the Trilogy ... "history repeats itself" ... The concept of "cycles" and the "Harvests" signifies that the Reapers have known for some time, that races and cultures "evolve" along predictable and repeatable "patterns". Javik mentions this when/if you take him to Sur'kesh, and the Prothean VI on Thessia also mentions that the "cycles" appear to be non random, and are not totally a Reaper contrivance.
So you will always have the same or similar cultures and behaviors each "cycle", you'll always have non-combatants, and always have population centers to harvest ... and apparently, always have quislings.
In other words, the Reapers are conducting an experiment on a Galactic scale over the course of Millennia to try and find the solution to their original problem. That being to stop the Galaxy from what they believe to be it's inevitable conclusion, the self annihilation of all life.
Of course you may see it differently, and that is yet another example of what makes us human 
...
Having said all that, I too would have liked to see the Rachni play a bigger role in ME3, but what we ultimately have here, is a now completed game, and this is nothing more than corporal punishment of deceased equines.