As for the idea of Cerberus in retrospect-
I enjoyed the concept of Cerberus far more than I enjoyed the particulars of the execution. There were always flaws with how they were presented (namely most of what was intended to make them morally dubious instead came off as incredibly stupid), but there were also some solid strengths. I don't think Mass Effect would have been as good without them, but I don't think it needs them going forward.
The most notable of which was the Illusive Man. As a foil, quasi-antagonist, and independent actor, he carried the trilogy further than any other antagonist character. Martin Sheen was an excellent casting for the role, and his performance in ME2 went a long way in establishing the tone, the tension, and the style of sleek danger and gain that ME2 relied on. I believe he was also important in ME3 because the Reapers have always been more of a context for the drama rather than the primary actors in the series. The Reapers, whether as a force of nature or looming danger, have been the backdrop against which everyone else acts, rather than the personalities themselves, so Cerberus and TIM having a hand in the drama of ME3 was consistent.
In ME1, Cerberus was a minor party and there's not much more to say. Their role and identity, as a rogue Black Ops group, made sense. If Cerberus didn't already exist, I would have demanded the setting create one. This was also the period at which they made the most sense in terms of scope and style: they relied on subterfuge and secrecy, covering their tracks, and their experiments were aimed towards potentially game-changing weaponizable breakthroughs. It fit the xeno-political tensions of the setting and the idea of Humanity as a rising/catch-up power that was challenging the status quo.
In ME2, Cerberus was expanded in a lot of ways. It was at it's ideological peak, in that it could articulate an ideology that many different sorts of people could agree with sincerely (including the Normandy crew), it wasn't blinded to the benefit of working with aliens and outsiders, and we had a number of good thematic points at which the premise of greater good for Humanity was both reasonable and terrifying when taken further. You didn't have to be a super-bigot to be willing to work with them, and while I dislike how we were made to work with them I feel it made sense that a private extremist group would be willing to focus on something smaller that the Alliance couldn't/wouldn't.
On the other hand, other parts of the Cerberus expansion made little sense. While the intelligence arm was interesting and semi-plausible in the 'it takes crazies to see the data in different ways', the financial and technological capability stretched disbelief. But the worst part of ME2 was that while Cerberus was ideologically sound, it was tactically incompetent. Instead of an organization of frightening competence and ability, the constant slew of disasters, failures, and resulting clean-ups by Shepard made Cerberus out to be a group of mad scientists and incopetents who could only succeed because of Shepard. Which applied to everyone, including the Alliance, but for a group that was supposed to be impressive it, well, wasn't.
ME3 flipped it all. Cerberus became tactically competent: a feeling not only reinforced by the well-balanced combat system and balanced enemies and military precision, but the way they fought in most of the missions encountered. The missions generally had a clear goal with an obvious gain, Cerberus success was plausible and even likely until Shepard intervened, and there were the other little things. Little pieces like Cerberus sabotaging the lift on Mars to hinder pursuit and falling back when defending the archives, or the suicide mission on Surkesh in which they call out positions as they track the target, and the entire propoganda effort on Grissom Academy. They fought and felt like a real danger that you had to take seriously when the bullets started flying. I even liked the idea of using the Collector Technology implants to make all their forces out of random people- that was an idea I think should have been coopted as a potential war asset gain or something.
But the ideology and strategy... it was a mess. Ideology was largely thrown out for the crutch of indoctrination, except apparently some undertones that the indoctrination was ideological in some manner. The Illusive Man claims a strategy, but precious little in the game ever clarifies how it was supposed to work or what most of the Cerberus missions had to do with achieving it. Cerberus lost all the ambiguity to become totally evil, down to the point of making all those willing volunteers of ME2 hired useful idiots to the 'real' Cerberus, while very few of their actions ever fit into any presented or plausible game plan for anything approaching a short or long term strategy. Control is never treated as a credible alternative, Cerberus goes around picking fights that only put more distance and resistance between them and their goal of Control, and Kai Leng made a terrible foil to Shepard. (Clone Shep was far better at that, even if it was just for the Power of Friendship.) No one else benefits from anything they do, not even other humans or some vague idea of human interests, as every act of sabotage or weakening other factions they do will become moot if they succeed (or fail) at controling the Reapers.
And the most galling point of it all was that there was no real need for Cerberus to be an antagonistic fighting force. Mars could have been the set up for Cerberus trading the Cruible plans to the Council in exchange for a seat on the Crucible project, and even most of the Cerberus combat missions could have remained with Cerberus being in a tense frenemy situation as a sorta-ally but not really of the Alliance. Cerberus in the Genophage arc could have been them working a secret deal with the Dalatrass to keep her hands clean, etc. etc. Look in my story corner for more.