I personally never understood why some people think ME2 was off point about fighting the reapers.

Alliance was sloppy about many things, but not the colonists. After (presumably, see ME: Incursion) the first big attack, they started arming colonies even technically outside of their jurisdiction with cannons strong enough to take down a cruiser-sized ship.

As I said, why send a manned mission (more than some scanner probe) into the middle of the Terminus when no one there is alive?

Yea is that why post every battle in WW2 US battle ships would extend massive fishing nets between ships to pick up all the dead bodies. They also sent subs down to the sunken ships to recover the bodies trapped in the ships.

The wiki shows precisely what I said; that they are the same. The STG commits immoral research and murder in the name of the salarian species and Cerberus does the same in the name of human species. What else is the STG fighting for if not to safeguard and advance salarian interest and thus power? You need influence to protect and advance your interests. We see direct evidence of this in the game.

Cerberus wanting humans to have more influence on the galactic stage, or even the dominant position, is the same thing. All species want whatever power they can get. If they didn't they'd have never persisted long enough to develop space travel. Once again, I think one can take serious issue with how effective or ineffective Cerberus is, whether they are a good or bad thing for humanity and its interests in the long run, and whether or not they have any real right to put themselves forward this way seeing as they are not officially sanctioned by the recognized representative of humanity. However that's a separate issue. The STG has official backing (mind you the League of One had official backing too) and Cerberus doesn't. Only primary difference between them.

Sure, that would be true if Mass Effect 2 was about Shepard fighting back against the giants of technology, information, media, and governments manipulating the public by controlling discourse. Mind you this is the same series that introduced us to the Spectres; elite government agents who can kill or torture you or invade your privacy at any time for any reason if they want to. Mind you, the game wants us to see these agents as heroes and not as villains to be fought against. The Council are the GOOD guys even if they are frustratingly bureaucratic. Mass Effect 2 would be exposing us to modern problems if it was dealing with gradual encroachment on freedom of expression, thought, and scientific freedom. Or perhaps if it was about mashing different cultures with values and customs and having them clash but then disallowing any real discussion of the issue much less tolerating any voices calling for a reversal of this trend, much less bothering to ask if anyone wanted this conflict in the first place. The closest we get to this is Samara's conflict with the cops on Illium, but even that is just presented as a hypothetical since the asari cops are only worried about an innocent human getting killed, in theory.

Mass Effect 2 isn't really written well enough to pose any genuinely challenging or pertinent questions. It's shallow. Oh, it tries, but it simplifies things too much, which coaxes most people away from thinking deeply about any issues being presented. Take Project Overlord for instance. It's hard to have a genuinely grey discussion on the merits or moral costs of the project because David isn't just used as a tool, possibly against his will, but he is being literally tortured both physically and mentally. Why exactly did the science in-universe demand that he be hoisted up on the cross and impaled with his eyes permanently held open like that? Would the climax be any different if after a few hours of hearing his screaming voice we reach the room he resides him only to find him laying on a hospital bed, sedated, only partially conscious? That make would make more sense. I cannot imagine any reason why he needed to be impaled all over his body except that the artist thought it made him look like Jesus Christ. It's very shocking, but it's cheap to do that. What if David wasn't suffering at all, but was still being used to control the geth? You'd still have a tricky question to answer.

Is this technology safe to use? Is it moral to use? Who should use it? What are the benefits and what are the risks? After a bad thing has been done and can't be undone, is it moral to use the fruits of that evil act to craft good acts? IE: do you use research gained through horrific means to do good or not? Does using it justify the inhumane research that was done? To be fair, I guess ME2 does tackle that one, though I still don't think it goes far enough or looks at the issue very fairly or with any depth. Perhaps the implications as to why the krogan can't be helped but with genetic manipulation has too many uncomfortable implications?

As I said, what Cerberus does and what the STG does and what the Spectres do are no different. It's right there in the wiki but you have to read it yourself and think about it yourself and make the connection, yourself. Do the games ever bring up the similarities between these organizations so that Shepard can pontificate about it, so that we the player can do the same? No. Even though it is blatantly obvious I doubt most people ever think much about how sinister the STG and Spectres are because they game never explicitly tells you to like it does Cerberus.

Now its too bad because ME2 truly COULD have done this. In fact, supplemental material for ME2 does talk about Cerberus using its agents in the media to manipulate the public and pass information between cells. The second novel has them murder a politician to advance their cause, which kind of subverts the whole political process. However again, this isn't in the games at all. Even if it were, it ought to be present this way; Cerberus is manipulating us through the media... who else is? Cerberus is influence the government with bribes and lobbying? Who else is? Cerberus is conducting inhumane experiments... who else is? Cerberus is assassinating people! Who else is?

There is room for depth there.

It's post-ME2, from when someone needed to finally define what Cerberus is. The salarians are nowhere near this, or at least not in the short run: their current military doctrine is to provide the turians with intelligence and let them do the fighting.

Yeah... it's like the difference between a pirate and a privateer... which is only that one is sanctioned by its government and the other is not.  It doesn't arbitrarily make the pirate or privateer any better a person... it makes the government that sanctions such actions worse than the government that refuses to sanction such things.

Why?  It's still irrelevant.  Just because their government sanctions what they do doesn't arbitrarily make what they do morally better than what Cerberus does.  Both experiment on species and alter them (immoral research) and both do commit murders.  The fact that they are sanctioned to do so by their government doesn't make those actions any less immoral.  Perhaps, their government is in need of being overthrown and replaced by a more moral government... a government that doesn't sanction immoral research and murder.  Were the SS any more "moral" in their actions just because those actions were sanctioned by Hitler's government?

Oh I see you are taking the stance that killing a terrorist who wants to detonate a bomb and kill 100 people is the same thing as just walking up and killing some random person on the street. 

That STG don't want to exterminate or subjugate all non-salarians but they have some persistent alliances is already a qualitative difference between them and late Cerberus.