DocSuess, you wrote a technically solid article, but I disagree with damn near everything and mostly for one reason:
You have based your entire vision of Halo and what it's supposed to be on this notion of HEROISM. It's almost as if you fell for the ONI propaganda that surrounds Spartans, that they're super powerful and save their fellow soldiers in a pinch and that Halo theme with the pulsating drums in the background makes us feel like we're doing God's work.
But if there's anything that Halo represents, beyond the fact that EVERYTHING WAS THE FLOOD, it's that humans are and have always been their own worst enemies. You said that you couldn't stand that John-117 had been made a walking war crime or that Dr. Halsey made a mad scientist, but ... are you serious?
You're talking about a woman who scoped out 75 six-year old children (through vaccination of all things), kidnapped them, replaced them in their families with flash clones DOOMED TO DIE. Let me repeat that for you. Kidnapped kids, replaced them with doomed mirror children. Augmented beyond human capacity, causing 30 to die (STILL KIDS HERE) and 12 to be crippled and washed out.
You don't want to think of John-117 as a walking war crime? Boo hoo. That's too bad. He is. Every single Spartan II was a war crime. No amount of whitewashing will change that. You're wearing rose-tinted glasses. Bungie never truly addressed the moral issues surrounding the Spartan II project and 343i, though still not where they need to be narrative-wise, have shown a greater degree of respect to the fact than I ever really anticipated.
You don't think that Cortana's motivations make sense? Fine. But let's not forget that AIs have always had the bigger picture in mind and have never hesitated to take things into their own hands if given the power to. See Mendicant Bias for more. I'm not saying she's right, or that the execution around her return and her plan are flawless, but they work, in the grand scheme of things.
I've stated in this very thread and others that I think there was issues with the narrative and character development in Halo 5, so I don't need to do that again right now. But Bungie's Halo trilogy dismissed the Master Chief's humanity and the sticky, unethical moral ramifications of the Spartan II program almost completely. You don't like 343's Halo? There are many that don't.
But to act as if the ugly background of the central characters doesn't count just because it doesn't make you feel "MASTER CHIEF, HECK YEAH" is damn near disingenuous. What it says is that you don't love the actual story of Halo, you just love a certain feeling you associated with earlier games and are not happy that feeling has dispersed since the propaganda has ended.