The majority of things in that thread is nitpicking at best, and largely draws comparison to the real world which doesnt make sense in the slightest when drawing comparison (apples to oranges) but i think you knew that already. Nothing in the trilogy (except cerberus bringing shepard back from the dead) was that far fetched by mass effect standards.
"I'll be running around and getting criminal status only to find a way to sneak few geth and krogans into Citadel, because I've lost my Spectre pass"
"I'll build Human Reaper, so it'll succeed where Nazara failed. I even gave it a third eye to be sure"
"I kill you, so you don't kill yourselves" (that's pretty logical though, I give him that)
Inventing a secret intergalactic Ark out of thin air is not logical or even remotely plausible in any universe.
Inventing something is illogical? I don't even...
out of thin air
You don't know anything about how it was done. You know only what Shepard knew. Everything in ME is "out of thin air", because it's fiction. Biotics, Mass Relays, indoctrination, FTL, quantum communication...