Paraphrasing, of course.
1. Why bother having collector baddies if there are reaper baddies.
They are a long, long way away though. The collector general is just another Saren, and the collectors are just the new geth. Another set of tools for the Reapers to employ, no?
2. Cerberus are evil in the first, grey in this one.
You're right, they never show how Cerberus is doing good in the first game. But then, in the first game you're working for the Alliance, why would you ever see or hear of them doing good?
3.Rebooting Shep. Crew return.
I thought they just did that as an excuse to make you work for Cerberus, no?
And the crew are Cerberus except for a few key characters like Chakwas. S'why Tali and Garrus are reluctant to work with them. Tali's even surprised by how nice they are.
4. Illusive man. Knowledge of and conversation options.
The lack of mention in the first game again appears to me to be intentional. Cerberus isn't really important in the first game, so why would you have heard of their leader?
But I do agree on the conversation options. I think it's because you both know there's nothing you can do about the situation rather than work with eachother.
5. Reapers:
a. Where were they?
b. Did they leave themselves other routes into the galaxy from wherever they are?
c. How long will it take them to get here and how many are there?
d. What happened to their Geth slaves?
e. What drives the cycle of destruction and how did it get started?
I think at least a few of these are answered in ME2.
a. Dark Space between galaxies.
b. Apparently not, as seen in the end cutscene. They've never been defeated before, why would they?
It's also conveyed in the first mass effect that the citadel normally activates itself, but the keepers evolved to only respond to the station, not the vanguard reaper. That's why he had to fly to it.
c. Doesn't really matter, does it? As you say, just two would pwn the galaxy, and a few thousand more years driving time is small compared to the 50,000 years they've been sitting there, isn't it?
d. The Geth are suffering a genocide at the hands of the council, "Mopping up" as Anderson (I think) says.
e. Granted. No idea. I guess that's for the third game.
6. Collectors:
a. Reapers suddenly like flesh now?
b. Where were they in the first game?
c. Master plan is stupid.
a. The reapers believe themselves above organics, but then I consider myself better than the pencil sitting on my desk. They consider them tools, nothing more, I think.
b. Good question. No idea. Maybe they thought that a whole geth armada would be enough, or it would've taken them too long to ftl jump to the citadel.
c. Agreed.
7. Abductions:
a. Why doesn't alliance care?
b. How can't they notice the motherfucking huge ship?!
a. Council states that the terminus systems are beyond their jurisdiction. They might care, but they can't do jack there. As Pressly says, "It's probably just slavers."
b. Yeah this is a good question. Any excuses I can come up with are pure speculation.
And Mordin's bug is a very astute observation. +1 Props. No idea how he got that.
The stuff you say about the endgame I mostly agree with.
8. Final Boss.
a. Organic= Metal... WTF?
b. Why 'reproduce' that way?
c. The point of it?
a,b,c. No idea. Maybe it's a pilot? *shrug*
Yeah, I agree with that whole section.
10. Wrapping up:
a. Only one way back. Dumb Reapers.
a. I think it's more arrogance on their part than short-sightedness.