ONI oozes "fuck it we'll do whatever we want." Like their entire history is taking the most heinous option available at every point. We don't know enough about Cortana's moral compass to compare, but I would suggest that the element of her possessing literal godlike intelligence does produce an inherently more interesting viewpoint. Ties into those old Divine Morality questions.
I would also suggest that your read on the pre-Cortana universe is simplistic. M'Dama, for instance, had literally nothing going for him in the way you're suggesting.
PS: Asserting something does not make it true, and the mixed Created faction is not the Prometheans in their entirety.
This really isn't true at all... and it's a an interesting position to take, considering Cortana is quite literally doing exactly what the fuck she wants and daring anyone in the galaxy to oppose her. She also taunts her enemies via intercom like a mustache-twirling Saturday morning super-villain.
ONI is an organization that's as assumed the responsibility of preserving HUMAN interests. The rationale of ONI leadership is to do what ever it takes to preserve humanity and minimize the risk of failure and minimize casualties. That said there are countless people
within ONI with different opinions, methods, and morale compasses.
Cortana and Warden (the ONLY Created "characters") aren't cartoon villains? Is BB a cartoon villain? Serin Osman? Naomi? FERO/Maya Sankar? Master Chief?
Yeah that's right our beloved Master Chief will make horrific choices if it means furthering the opportunity for humanity to survive. Who'd he learn that from? ONI- and it was a lesson that saved the galaxy.
Remember that time Chief lead a Covenant fleet to a secluded Insurrectionist colony, deceived them, then stole their only hope of escaping the impending Covenant attack, leaving every man woman and child to die a horrible death? Totally fucked up.... totally neccisary.
Cortana and her minions on the other hand are robotic and cold. Ensuring 'peace' through intimidation -murdering scores without warning- without even a chance to comply. Her omniscience is the least interesting aspect of it all, as it's totally cliche. How many AI uprisings due to society being to stupid too police itself can Sci-FI handle!?!?
Also, How can you say M'dama had nothing going like I suggested? He
was an awesomely deep and cunning character before he was wasted by H5s terrible writing. The reason he opposed 'Vadam's leadership- because he felt that humanity could not be trusted in the newfound alliance. He was exactly right! while Thel was signing peace treaties with the UNSC, ONI was selling arms to his opposition, and bioengineering a poison food crop to cripple the Sanghelios homeworld.
ONI of course had strong justifications for these things- why should they ensure victory to an Elite who was paramount in the near destruction of the human race? Why should they let help the Elite's regain a foothold in the galaxy, and risk them become a powerful enemy again?
The Halo Universe
was a lovely mess of factions who each had every reason to view themselves as the good guy and each other as the bad guys. Now it's boringly clear who the bad guy is, and the new bad guys motives are totally unearned. She just shows up out of nowhere with a new 10,000 year plan she 'calculated' thanks to a CPU boost from a macguffin.