Terminus Pi wrote...
if you take too long to go to the collector base, all your crew except for Dr. Chakwas are "liquified". However, in the cinematic, you save several crewmembers from the pods and at the part where Chakwas says "what about us? we can't fight", there are some behind her, when they should be dead.
According to ME2's story, the collectors are abducting humans because reapers are part machine and part organic fluids. It also states that reapers take the form of the race that "fuels" them and that's why the final boss has a "human" shape. However, EVERY single reaper we see has a squid-like shape. Sovereign was squid shaped, the end cinematic sequence of ME2 shows a whole fleet of squid-like reapers AND in one of our dialogues with the Illusive Man, he says that the derelict reaper is "a 35 million year old derelict reaper" - and guess what? That one is squid-shaped too.
So, in at least 35 million years they have come every 50.000 years and wiped out all organic life, but they never took any other form than that squid shape. And now, all of a sudden, they take the shape of the race that they use? I guess the galaxy has been quite abundant in squid creatures.
My theory is that there's the host-body inside the enormous shell. Its the only thing I can figure to explain the end of the game.
Because look at the size of the Human-Reaper. He's nowhere near the right size. Makes more sense that the squidship develops/is built around him.
1. It is never explained how the Collector ship knew where to find the original Normandy. You know, the stealth frigate. - Its stealthy by the standards of the Citadel dwellers. It's stealthy compared to the Geth. I'd imagine the Collector ship just has more advanced sensors (Or, they looked out of the window. Remember, they're not the Geth. They actually have windows). Its not like it was a perfectly planned ambush, I figured it was more a case of shred some ships in the area and wait for Shepard to turn up.
3. If we count the vorcha and rachni as races the reapers want to eliminate, and assume that all relay using organic species are also on the hit list, there are 13 sapient species for them to wipe out, 14 if we include the geth. 50,000 years ago, there was one; the Protheans. Only maybe makes sense if the Protheans really did "Enkindle" everyone else. - That's actually my reason for accepting that theory.
Plus, there's the possibility of luck. Or the Protheans being warmongers who committed mass genocide when they discovered life at the level to threaten them.
As to why the Collectors didn't er... collect Ash/Kai - They're bait. It makes more sense to leave the bait in the open as long as possible. So they're last to be picked up, to give Shep something to go for. Then he turns on the big guns, the Collectors, not expecting EDI go "Ohshi-" and run off, without time to grab their bait back.
Regarding population numbers - I don't know if we can imagine how human population numbers would spike given
a) Plentiful resources
and

Better medical care
Cut down the childhood mortality in the poorer countries, and encourage bigger families among the heavily industrialised ones, and you've got a recipe for massive growth. I don't know about the numbers given, as they do seem a bit farfetched.
Darth Drago - They seem less plotholes, and more "things that irk you". They can pretty much all be reasonably explained (Particularly 4, where you seem to just explain the reasoning behind the comment :/ Maybe look at it from a less human-centric view, and more at the awesomeness of Justicars, who just don't work with anyone. Plus, the Collectors are so rare as to be considered myth, but should pop up on a few more planets? Also, remember EDI had her functions limited at that point in time. Maybe TIM didn't want her able to break Cerberus encryption easily)