I never understood where the love people have for Cerberus comes from. They were clearly a terrorist organization bent on truly horrifying research in the first game.
In the second, TIM treats everyone simply as tools to carry out their tasks and then be discarded. 95% of ME2 is simply team building for the final mission. A mission where if you don't capture the station like TIM wants, he effectively says you failed. His intention was the station the whole time.
Some keep saying they changed into the 'bad' guys in ME 3. They were always the 'bad guys'. Everything in the first two games was just building to this apex. They were consistently looking for ways to create and control super-soldiers. Everything they ever did was to grab more power for themselves, right up to the end when they wanted to control the reapers themselves for the power it could give them.
Don't know about the others, but with me it's not the "love for Cerberus", but rather my dislike for Bioware's naive stance on morality in politics and shadowy affairs.
It's like Bioware is trying to push the idea that if you are a "good guy", you can just power through everything with your Awesome Paragon Powers.
There is zero acknowledgment to the fact that politics and spy games between nations - and most certainly between different species alien to each other,
are a dirty affair, occasionally dotted by conspiracies, murder, blackmail, frame jobs, cyber warefare, psy-ops, etc.
Alliance Intelligence was nothing if not an example for incompetecy throughout the ME story, with virtually next to no useful intel coming from their direction. By all rights, Humanity should have had an organization to fill the void and counter its counterparts.
It could have been Cerberus if Bioware didn't make them into the over-the-top incompetent villains that they were.