Frankly I like how the game deals Cerberus with bits and pieces. And with limited perspective from Shepard, you're not sure what is right and what is outright lies.
In ME Evolution, Jack Harper have his own idea about Cerberus and after being exposed to reaper artifact, he still retain his sanity for several decades. I think he's kinda like Shepard in the beginning, he wanted humanity to be prepared to the eventual reaper invasion and he amassed an army for it. But he views the reapers as potential to further his ideals about humanity's advancement, embrace their tech, try to learn what they are and he wanted humanity to extend what it could achieve on its own through the millennial worth of knowledge from the reapers. In that essence, he is ambitious but he desire to be the omnipotent father of humanity, .
Within Cerberus, there's political, science and military division. It was likely that the military division is an off-shoot of Alliance Systems who didn't want to play nice with the alien races especially after the war and they simply siphon off the Alliance military in all the years. The best portrayal of this is in The Expanse' fourth book, Nemesis Game.
The science division is something that was particularly interesting to me. Almost every Cerberus scientist you met have a skewed morality and ethics and they're well-aware of the risk and limitation but do it anyway even if it results mass death.. kinda like attitude among certain scientific community during the world war and even us right now with dealing with embryonic stem cells. Unfortunately, the game doesn't explore much about how things works and it was simply easy enough to wave space magic (especially Shepard's reconstruction). But in the game, I do think it was neat that certain companies like Binary Helix and even ExoGeni have connections directly to Cerberus. And the Akuze background show that Cerberus was well aware of who Shepard was and the experiment done on Corporal Toombs was about making him into a super soldier which mirrored what Cerberus done to Shepard in ME2. So it wasn't that odd for me to assume Cerberus have monitored Shepard almost the entirety of her career to be able to reconstruct in two years... heck I still have my undergrad friends who haven't finish their Masters yet since 2011, science doesn't happen in a snap.
As for the political faction, you could assume Udina was secretly supported by Cerberus from the start. Which kinda make sense why he make his move to try to get the alien councilors killed. And I always assume Miranda's father was always supporting Cerberus from the beginning as his desire to expand his legacy through science is very Cerberus-ey. And I canoned that he knew all along where she is and she was doing exactly what her father and TIM expected from her except that she kept her sister away from Cerberus knowledge until she use her Cerberus connection to keep her sister safe.
Either way, I have no trouble with how the game portrayed Cerberus as whatever. And I recommend reading the Expanse series, the current tv series season only deals with half the first book so the good bits was in season 2.