The Citadel trap

Not really.

Which is odd because people call that catalyst the biggest plot hole in the story. Which ignores this planet sized one in the first game.

Lol Chorban discover mostly everithing about the keepers with those few scans, even the cycle period !
This is the letter he sends to Shep during ME2 :
"
From: Chorban

I hope this address still works. I promised to send you intel on the keepers if I found anything, and this is important. See, those scans you took? It turns out the keepers are bio-engineered... and based on my comparisons to some of that material from Saren's flagship Sovereign, they were engineered millions of years ago... by the same people who made Sovereign!

You may not understand how important this is, but it suggests that the Citadel wasn't really made by the Protheans! It may have been made by something far older, with the keepers as organic guardians. And what's more, based on my genetic readings, they're supposed to react to... something, some signal or something... about every 50 thousand years. You can measure genetic variances; it's a bit like comparing rings on a tree to see the drought years.

Whoever did this... well, around the last time this signal went off would be around the time the Protheans disappeared. And it's scheduled to go off sometime around now. If any of the old tech still works, they could have some nasty surprises waiting for us.

Just thought you'd want to know. Nobody here on the Citadel will listen to me.

-Chorban "

That looks like the major plot hole in this cycle of reapa destruction imo

I usually thought of the whole keeper thing as evidence that, originally, the story, even within ME1, was planned to go in a very different direction than it eventually did.  ME1 also makes mention of the Citadel itself actually being an enormous mass relay... and it is never actually shown to be one or used as one.  I've always suspected that the bit about the Mass Relay statue being a little one-way relay was added into the story somewhat later in the development cycle after the development team threw out an original, larger idea utilizing the whole Citadel as a mass relay.

I was ready to accept the unevitable
 but

yeah, i guess Drew K. might have had something in mind

And indoctination must play a role here clearly.

It's not odd if the Keepers actively deny access to those areas. It wouldn't be very good for business if those pesky organics found the part of the underbelly that the London Conduit leads to; the place where they make new Reapers. I feel like the Keepers denying areas was confirmed at some point, but I don't remember.

My thoughts exactly, especially after that conversation. The Citadel is a Reaper device, after all, so low-key indoctrination would make sense to keep the galaxy's leadership pacified. It would make the council less stupid, as well, but it doesn't excuse the rest of the galaxy from being so stubborn about not believing Shepard and co.

"It's not right. It looks pretty - calm and peaceful - but it's not right... It's all just an illusion." I can't help but think of synthesis when I hear that line.

That's a good point. "You evolve along the paths we desire."

I agree it s logical to put the government in the zone, even on the citadel, but not before knowing the place a bit !
Like where is the control center ! (wikia quote : "The location of the Citadel's core and its master control unit, regulating systems such as life support and navigation, remain hidden.")
What are those worker dealing with everything ?!?
Indoctrination is the most likely response but hell, u could easily have an entire game/book about the discovery of the citadel by the asari. So much to be understood and discovered.