I suspect that was kind of the point. Were they pure evil? Were they just overboard? Was it bad press? Did the left hand know what the right was doing? Or were you being seduced? Or corrupted? Or fleecing them?The Cerberus aspect also makes no sense given that Shepard constantly messed with everything of theirs that she came across, and worse yet, depending on the background you picked for your Shepard, they could have been a victim of one of their messed up experiments. Not to mention how they went from a rogue military black-ops group that did their best to hide, sourcing their ships and planetside habitats from multiple sources so they won't be traceable, etc. to being a loud and proud privately funded organization that slaps their logo on everything, to being a huge army that you have to fight more often than the Reapers that are invading the whole galaxy. I really couldn't get over all the hand-waving that was done to excuse all the frankly evil stuff you learned about them doing in the first game to convince you they totally weren't an evil organization to just give up on that for the next game anyway.
I found it a very interesting set of circumstances to play out, especially after the white knighting of Shep in ME1. It very much was a 'how far will you go' moment. A lot of that evil was swept under the rug as 'rogue elements' by Miranda and the Illusive Man, as you'd expect.
The shift from gray back to black after the end of ME2 before ME3 began was very jarring by comparison. I suspect the designers intended it to be a road to hell paved with good intentions moment, especially with the Reapers using the Illusive Man as their catspaw. But they needed more foreshadowing, and more of the 'bad Cerberus' from ME3 incorporated into ME2 to really work that storyline.