My opinion is, in order for bioware to make ME2, it had to dismiss the reaper threat and turn everyone who knew about it into an idiot, in order for the plot to make sense. Liara doesn't care, Ashley doesn't care, tali, garrus, wrex, shepard, TIM anyone...
They contorted the setting to prop up railroading Shepard into joining a terrorist organization because someone at BioWare (I think we know who) couldn't handle just letting Cerberus rest with Mass Effect 1 or that the first game had better set them up as enemies if the group was to continue in the series.
In ME1, they were a rogue Alliance covert ops group that only top military personnel know about, who murdered a bunch of Alliance soldiers, and did horrifying experiments. Shepard hunted them down, discovered they killed an Alliance Admiral, and found out they were responsible for the massacre on Akuze. Pretty important if your Shepard was a Sole Survivor.
Oh wait now they're a pro-human group whose ends (don't actually) justify the means, have galactic influence, and everyone knows about them. Their background has changed and all the crap they pulled, that was just misunderstandings or rogue cells or some other bullshit from Miranda. Quick look at her ass so you don't realize there isn't a dialogue option to ask about Admiral Kahoku or them killing Shepard's own unit.
This is quality writing. Aren't you impressed by how dark and morally ambiguous this all is? Shepard does whatever it takes to stop bugs from kidnapping farmers to make a robot that can be killed with a handgun.