Things that don't make sense (v2)

If Kirrahe is alive in ME3 and Thane wasn't recruited or died in ME2, Kirrahe will say he's been assigned security detail for the councilor. If Thane is in ME3, Kirrahe won't make that comment. Why? How would anyone know that Thane would help the councilor during the coup? Had Kirrahe been with the councilor, the standoff with Kai Leng would've played out much differently or at least I would believe it would.

It made no difference. You mentioned Thessia. Without the thorian, the asari couldn't do much.

Speaking of the Thorian and the Rachni, both of those species didn't appear to ever have a need to create synthetics due to their unique physiology, and both could arguably be said to be immune to the effects of Reaper indoctrination. If we were to excuse the factors of the other species present in the galaxy, I wonder if the Reapers would have left them alone, despite their relatively advanced state of sentience?

Would the Catalyst even tolerate two examples of a biological species not falling into it's neat little world-view, or would it exterminate them and then sweep their contradiction to it's experiment under the cosmic rug?

EDIT: Sorry, got the wrong quote.

Lol... we're crossing paths here.  I really need to get my eyes checked again.

Sure, I'll buy that.  Still... leaving the warning about the Citadel being a trap out of the beacon message only ensured that even if the Asari or anyone else had discovered the Thorian on their own centuries earlier or even if they had found some other way to translate the messages inside the beacons, the needed warning about the Citadel being a trap just wasn't in there to be heard.

It was willing to use the Geth to kill off the Thorian and had no qualms about turning the Rachni offspring of the Queen into husks while also imprisoning her, so it's certainly wasn't interested in "preserving" such anomalies either. I mean for an intelligence supposedly based on cold hard machine logic you'd think that such a blatant example of organic life existing outside of it's little "experiment" would at the very least give it pause.

Haha, ok, I think we are all sorted out again now.

So yea, I agree, the Ilos crowd should have added the Citadel warning into the message. It's been a while since I played ME1 so I am not sure how exactly the time line was.
But if my memory serves, Vigils speech could be interpreted like this:
- Reapers invade through the Citadel relay, kill the leaders and disrupt the relay network and all communications immediatly.
- The Ilos crowd realizes that an invasion is happening buthas no real idea about the details. They go into hybernation
- They wake up a few centuries later, realize that the reapers have gone and send out a message that just says "Hey, whoever survived the reaper invasion, we are still here on Ilos."
- No one replies
- Upon realizing that they are the only ones left, the Ilos crowd tries to reconstruct what actually happened (by what means is unclear). Over the next couple of months/years, they figure out the citadel trap.
- At this point, they could send out a second message but they don't. It's unclear why. Maybe they didn't have the power left to do so and still go through the conduit. Maybe they thought that only protheans could get the message anyway, so they didn't bother (not knowing about the Thorian). Wharever but they didn't
- They go to the Citadel, sabotage the Keepers and die there.
=> Only a message was sent saying "Hey, we are still on Ilos". because that was their only concern when they sent that message

The second possibility would be that the warning about the citadel actually was included in the message but it degraded over 50.000 years and while Shepard has the Cypher, s/he still cannot pick up the message perfectly. This also makes sense, given that ti does take 2 beacons to garble together enough of the message to even only get the idea that the Protheans were on Ilos.
Now, IIRC, Vigil never mentions anything of that sort but he never goes into much detail about the message anyway and who can blame him, seeing how urgent and time sensitive the situation was at that point.

So I agree, technically the Citadel should have been in the message but I think there are more than enough loopholes to explain why it was not.

Speaking of the Thorian and the Rachni, both of those species didn't appear to ever have a need to create synthetics due to their unique physiology, and both could arguably be said to be immune to the effects of Reaper indoctrination. If we were to excuse the factors of the other species present in the galaxy, I wonder if the Reapers would have left them alone, despite their relatively advanced state of sentience?

Would the Catalyst even tolerate two examples of a biological species not falling into it's neat little world-view, or would it exterminate them and then sweep their contradiction to it's experiment under the cosmic rug?

So, the Conduit project is underway before the attack... This, of course, begs the question... Why?

ETA:  I wanted to also add in this line from Javik:  "It seems you believe the Protheans built the mass relays.  The Reapers are cunning in their deception."  Since Javik was put in stasus before the end of the Reaper War, this again shows that the Protheans were fully aware that the Citadel and Mass Relays were a trap built by the Reapers.  Again, showing that the group on Ilos had ample opportunity to include a specific warning about that trap in their beacon message.