Shepard the Leper wrote...
1. Immortal beings that simply "are" (according to Sovereign) who need organics (humans only in this case) doesn't make sense at all.
2. Why do immortals need reproduction?
3. WTF?
4. Sovereign says something different. Maybe they're both lying, who knows. Arrival also happens between ME2 and ME3. It isn't a real part of ME2.
5. Depending on Shep's background, your Shep might be the only survivor of a slave raid. Colonies dissapearing isn't something new and it's definitely not related to the Reapers. In fact, it would be an incredibly stupid thing to do, considering the Reaper's efforts to erase all traces of their existence. Colonies vanishing is a good way to draw attention. You don't want that 
6. Who made them "mindless"? And why? Slaves are always used to do the dirty work. Why do the Reapers need them?
7. The Collectors are Reaper builders now? They've done a poor job doing nothing for 50k years before starting to build one. Sovereign's failure was expected by the Reapers?
8. I've no idea where you got that idea.
9. Wiping out all life every now and then isn't a goal. That's sadistic, but that's all we know. Everything you've come up with is imaginary.
In addition to what ark said,
1. First of all, you're taking soveriegn literally when he has every reason to exaggerate or omit facts. He boasted that any attempts to stop him from activating the citadel were doomed to failure, and that wasn't true. Is that a plot problem too? Soveriegn he has absolutely no reason to tell you the truth. Like Obi wan has no reason to tell Luke that Vader is his father. So he lies.
More to the point you can both despise and depend on a being at the same time. The two things are not mutually exclusive at all. There was a similar setup in the matrix. Or look at real life.
2. Immortal or not, why wouldn't they want to increase their numbers? Failing that, they have a fallen member to replace.
3. I still don't see any argument except "goo is silly." Fine. But why is it a plot problem?
4. What did soveriegn say that contradicted anything?
5. The only other ones who'd take colonies are batarians and geth, and hitting so many so fast "without a trace" is not their MO. Then consider the timing and there's one obvious answer-besides, as I said, ME1 had leads with weaker connections. Plus, they did kill Shepard before starting, and as it turned out, without him nobody cared about the colonies.
6. Ark covered that.
7. What ark said. And soveriegn's death clearly wasn't intended; I have no idea where you got that. The collectors obviously expected to be operating with the help of the reaper fleet. With soveriegn dead, they have to go it alone, for the moment. Exactly why the HR couldn't be delayed I'm not sure, but there are many possible explanations. It all depends on the reapers motives, which we don't completely now. Maybe they thought the timeframe wouldn't be long enough for something bad to happen, especially with Shepard dead.
8 & 9. Like Ark said, you're demanding to be spoonfed here. If there's anything to have unanswered questions about, it's the lovecraftian robot gods. My point is that we have enough information and heavy implications for the plot to make sense.
Shepard the Leper wrote...
1. My view what a Reaper is doesn't fit ME2's Terminator explanation. In ME1 it looks like the Reaper (Sovereign) takes control over Saren's body. The moment Shepard "kills" this Saren-Reaper, the ship's shields fail and it is easily destroyed (killing the Saren-Reaper destroyed the ship). In ME2 we see something telling the Collector general he's failed and it leaves. To me that looks like Reapers are not machines with different parts, but like "spirits" with the ability to control / use advanced machinery and/or organics.
2. True, but it remains a mystery how your squadmates draw that conclusion. I would have preferred to obtain this information by checking their systems or through interrogating a Collector.
3. The Reapers are way too interesting. I want to get to know them a little. The danger is obvious, but there are no motives except some speculations in both games which we have to assume are true. I really liked how you discovered the Reapers in ME1 although the game revolved around tracking down Saren. Some solid info about why the Collectors are doing what they're doing and the connection to the Reapers, or at least a good lead to go after the Collectors at the start of ME2 would have made things a lot more convincing imo.
4. There's lots of stuff that could have been done better regarding ME2's main plot. To me the whole Collector issue was little more than a distraction from ME2's strongest aspect - the characters. A better main plot would have made an already great game slightly better. I do hope ME3 will have a solid main-plot and isn't about building an army only. That would be fun enough, but I expect more from Bioware.
1. It's made clear that the collectors have been heavily modified and implanted over centuries, unlike Saren. The irony is that despite being organic bugs, the collectors are more like likeless automations then the geth. At any rate there are many possible explanations as to why the two modes of control work differently. Different reaper, different host, different implants, both at once?
2. The volume of the ship's transportation capacity made it obvious the collectors were eventually intending to attack large population centers. The question is how; Arrival explains that.
3. As ark said, some questions are obviously being left unanswered. ME2 was clearly intended to set up questions then answer them. I understand why you would want more, but the point is that we don't really
need more. There's a difference between "could have been done better" and "broken."
Also, I seem to recall someone findng in-game files holding some exposition on the relationship between the collectors and the reapers in the collectors' own words. Or something like that-I'm not sure. The devs considered further exploration on the issue and cut the content for whatever reason. So it's not like the thought never crossed their minds, and the writers obviously wrote it. And since they were the ones making decisions on the field, I'm inclined to trust their judgement.
4. Whatever the result, the collector issue was intended to be a plot point to gather the characters around, and makes sense in principle at least. Otherwise, agreed.