I agree that TIM wasn't speciesist. As far as I remember he has no dialogue in either the games, books, or comics that could be considered as bigoted. He's just a hard core human nationalist, but other than wanting to see humanity at the top of the galactic scrap heap he has no animus towards aliens. Having said that, Cerberus did attract a lot of knuckle-draggers. Kai Leng wasn't an outlier, and I think TIM turned a blind eye to that element so long as they served his goals and remained useful.
Miranda, even though presented as something of an Ice Queen at the start of ME2, comes across as far less cold and calculating that TIM. Underneath the cold exterior she's even something of an idealist, and has a romanticized view of Cerberus that is slightly out of step with the reality. Were she to take the helm of an organization similar to Cerberus, I have a feeling it would more closely align to what she wanted Cerberus to be rather than what Cerberus actually was.
As for mustache-twirling evil...Cerberus had that in spades. Most of the encounters with Cerberus in ME1 revolved around Mengele-like experiments gone awry, and one of them is a potential origin story for Shepard.
I also cannot find anything in ME lore regards Jack Harper/TIM being bigoted either. I would even argue that he was totally nationalistic; many Cerberus efforts involved cross species co-operation, and their impact the gains in technology actually lessened Human influence by enhancing the military and technological capabilities of recent enemies and uneasy allies who had force superiority encoded and enforced by treaties.
Cerberus initiated the design of the SR-1 and developed technologies that made the Turian and Salarian fleets far more capable a force. The same Technological Industrial complex that provided that advance is the most likely candidate to have developed the Thannix canon which was one of the singular weapons advances in the final years of the cycle.
Looking deeper into the timeline of events featuring Cerberus in ME1 and the accusations of Mengele type behaviour.
From my POV, the Thorian infected the people that were turned into creepers on the Cerberus base. Looking closer at the timeline of its discovery suggests more that Cerberus investigation into Thorian Creepers may not have been so evil and immoral
The Thorian's ability to enthrall others and create creepers was discovered in 2183 by the Exo-Geni corporation who refused to warn the colonists; choosing to observe the results. In less than a month, 80% of the colony had succumbed to the Thorian's painful way of conditioning. We met some humans; but there were far more creepers than colonists. The spread of Thorian infection isn't detailed, but the timeline suggests that a Thorian infection is something dangerous and fast acting to humans.
The Mass Effect 1 timeline starts in 2183 and the encounter with the Creepers encountered in the Cerberus bases occurs within weeks/months of the discovery of the Thorian's danger to humanity. The Creepers were at advanced state of the disease and as such had more likely been exposed to the Thorian in the early stages. Cerberus use of them may actually be for totally different reasons than their are at face value.
The responsible course of action was to try and quarantine the infection (Something Cerberus did) and establish ways of curing it before the degradation into the Creeper state is total and investigate innoculation etc. Failing that, in the advanced stage of infection that is the Creeper State, investigating some form of use that could prevent further loss of life. This would include testing the capability of a creeper in war. The person that is now a Creeper is essentially dead. If one soldier is able to be saved by the sacrifice of the creeper; or a colony world innoculated against a deadly and terrifying disease, then the sacrifice of the walking corpse is worth-it.
The Rachni investigation was justified IMO; if only to find a counter measure to a known enemy's tactics of developing biological weapons. Even without the indoctrination, Saren Arterius was an avowed enemy of humanity who Jack Harper encountered earlier. I believe that TIM's manifesto was inspired by his encounters with Saren and that he paid extra close attention to his actions and investments.
The Akuze encounter was a first contact with an unknown species. The Alliance were more responsible for that failure and I do not see anything suspicious in Cerberus Black Ops being deployed in an observational role. Also I do not believe the testimony of Toombs to be fully valid and beyond question. His actions in seeking revenge suggest an unstable mind and we have no information to indicate his condition when discovered; most probably he was severely injured and traumatized. Cerberus employed some of the better medical care available in the Alliance and probably saved Toombs life. His description of being tortured by injection of Thresher Acid seems a bit suspect, there was already plenty of evidence of the effects of Thresher Acid on human tissue available and it would have been an extreme waste of resources to treat a severely wounded and traumatized soldier to obtain data that was already available far easier.
Kohoku was involved in espionage against his own species and military command for personal or ego motivated reasons. He may have been trying to gain a form of justice for his men, but the sort of revelations he was willing to release would have damaged the Alliance far more than the loss of a few marines. He condemned himself as a prospective whistle blower and had to disappear quietly. Cerberus got to him first, but I don't believe that the Alliance would have been far behind them, nor that their reconciling of the problem would have been any different
The treatment of the children on Pragia plays more like simple human frailties and fears being manifested in an institutionalized setting. I don't condemn an organization for the actions of such a facility. I had an experience of institutionalized abuse in a child care setting as a kid; the organization was run on charitable grounds to care for disadvantaged kids, but the staff on the front line did not live by the ideals of the organization in the slightest.
I feel the situation on Pragia for the kids was also inspired by the prejudice and fears against biotics and the ability of a biotic to overpower a physically stronger being shifted the instincts of Power Roles. For most of human history, adults exerted control over kids through physical authority. The reversal of that instinct can lead to all sorts of abusive behaviour
In ME3, Cerberus became indoctrinated and are more victims and war casualties like all the others that were compelled, against their will and without consent, into acting in concert with the Reapers.