Them questioning shepard has probably been the smartest thing any character in mass effect has done in a while. "I work with cerberus, only I don't" isn't a good answer and doesn't explain ****, nor does it make the new normandy, edi, the crew, or shepard himself, any more trustworthy in any capacity.
Shepard was either dead, or as close to dead as possible, for two years while be worked on by an organization known for their shady operations, human experimentation, unethical abandonment of all restraint or scientific caution, and has confirmed tech implants and experimental medical tech inside of their body, as well as having a revolutionary procedure preformed to bring their biological body back to fully functional. In an age where an artificial or virtual intelligence can have a persons brain patterns copied, stored, and uploaded into a physical body (President Huerta), why don't more people actually question shepard as to whether they actually are shepard? Where is the proof cerberus didn't implant mental of physiological alterations to make shepard more complaint? A ability to basically turn off shepards implants or worse, begin influencing shepard mentally through chemical and neural signal alterations in the brain at key points? Aria is like the only person to do so, and all she did was pretty much a once over using a scanner. That is also not good enough, in my opinion.
I don't understand how people don't like the VS questioning shepard, when this one question of whether shepard is really shepard, or is completely free of cerberus interference, has never been addressed or brought up in any serious or in depth capacity?