Mass Effect 2 Plot Analysis

Twenty Sided's Shamus Young has kicked up a three-part, spoiler-heavy analysis of the storyline in Mass Effect 2 (here, here, and here). While some of you may not entirely agree with him, he does shed some light on the plot holes present in BioWare's sci-fi sequel by pointing out issues with the game's beginning, conclusion, and how it seemingly goes against some of the understood facts of the original. Generous excerpts below:
In game 1, they firmly established that the Reapers were machines. The Reapers had nothing but contempt and disdain for flesh. Then Mass Effect 2 comes along and suddenly the Reapers actually have this supply of organics. In fact, their entire plan seems to involve mostly organics. They maintain this army of organics that live on a barren asteroid base for millions of years (the collectors are actually what's left of the last race the Reapers conquered) with nothing to do but stare at the walls as the eons tick by. (I guess they ordered pizza when they got hungry?)

The collectors weren't mentioned in the last game, which is kind of odd since that means the Reapers left the Collectors and all their weaponry sitting around doing nothing while Sovereign attacked Citadel Station alone. And didn't win. I'm not saying there can't be a good answer for this stuff, but that they don't even try to give one. They don't even lampshade it by having one of the good guys speculate.

...

At the end of the game, you have control of the colonist-liquefying Slurpee Maker of Doom. You have a conversation with the Illusive Man and you are offered a choice:

1) Keep it so that Cerberus can study it.
2) Ignore the Illusive Man's request and obliterate the base.

...

I find this line of reasoning to be lazy and infantile to the point of being offensive.

1) Proof. By this point you have now spent two whole games trying to convince the rest of the galaxy that the Reaper threat is real. One of the major reasons the battle is so desperate is because you've been working alone. Here is unambiguous proof of an advanced enemy with hostile intentions.

2) Memorial. Keeping the facility is crucial for understanding who died here, and how. If nothing else, looking for bodies and dogtags to send home would have been worthwhile and offer some families a sense of closure.

3) Technology. Yes, study the technology. Just because the Slurpee machine of evilness is horrible doesn't mean that we shouldn't understand how it works and why. Particularly when you're in a war and the enemy has you outmatched in both numbers and tech. The idea that we shouldn't understand a technology because it has been used in evil ways is a line of reasoning that borders on primitive superstition.

4) Intel. How does the enemy communicate? What is their history? What are their plans? Up until now the Reapers have been a great big question mark, and this is our first chance to fill in some blanks by digging around in their computers and reading their mail.

...

But the main problem problem is that the game will only let you give the tech exclusively to Cerberus. This is a false binary choice: Give the Slurpee tech to Cerberus, or blow up the most crucial source of tech and intel since the war began. The most responsible, sensible, and pragmatic course of action is the one the game won't even let you consider: Keep the station and show it to the Alliance, the Council, and whoever else might want a tour of the place. Since your ship is the only one with the tech to get here, it should be up to you who gets to visit.

I haven't seen a moral dilemma this forced and this false since the end of Fable, where you could DISCARD SWORD or TAKE SWORD AND STAB SISTER, but not TAKE SWORD AND WALK AWAY. For shame, BioWare. You're better than this.