The thing about “fixing” the show is that I do understand why they’re not tackling many of the ~ideological~ issues at its heart.
SHIELD has to be positioned as (more or less) a “good” entity in order for AoS to work as a mainstream entertainment show attached to the MCU. Also, it takes a lot of inspiration from American law-enforcement programming, a genre that tacitly endorses things like police brutality. So if I were to magically gain control of AoS and its writing team, and didn’t have to worry about advertising or ratings or editorial input from Marvel (LOL), I’d introduce way more scenes where people have personal ethical dilemmas about “doing the right thing” as a SHIELD agent.
Most of the characters in AoS rely on Coulson for guidance or orders, but Coulson himself is definitely someone whose own moral code was tied to… receiving orders. He’s portrayed as ~good guy~ but we know that he’s spent his entire career treating SHIELD almost like a religion, convinced that they’re the best hope for protecting humanity against alien/superhuman threats. Except all the while, SHIELD was infiltrated by Hydra, and SHIELD itself was doing some pretty shady stuff even in its day-to-day business.
I mean, I think that the most “accurate” portrayals of SHIELD were from outsider perspectives in Iron Man and Thor, where we see Coulson and Fury invading people’s lives, confiscating their possessions, and spying on them. Whereas AoS looks at SHIELD from the angle of a team of lovable characters, and doesn’t really touch on their moral ambiguity except in the case of field agents who literally kill people.
So I’d probably see Skye begin to think for herself about what SHIELD actually means (other than in the personal sense of it being her first real “family”), possibly through a series of conversations with May, who would give us a more in-depth look at the darker side of SHIELD. And we’d get to see more of the side of FitzSimmons where they care so much about a new invention or discovery that they forget about its potential human impact. Another good idea would be regular check-ins with civilians who are on the superpower list, and how SHIELD has helped or hindered them in their daily lives. Essentially, we’d see more of the real-world effects of SHIELD’s work, and we’d see how the characters react to that information.
In a general worldbuilding sense, I’d like to know way more about how the leak at the end of CATWS changed public opinion of SHIELD and superhumans/aliens. And that would include the more “innocent” characters like Skye and FitzSimmons finding out about the really shady stuff SHIELD was doing behind closed doors, and pressuring Coulson into creating an environment where agents could be held more accountable. This could be helped along by them finding out that these things are ALREADY happening within the confines of the tiny new-SHIELD, perhaps with some of the mercenaries torturing prisoners for information, or someone using alien tech to stalk their ex-girlfriend, or whatever.
Either that, or some kind of story arc where the writers make it clear that the whole team are such true believers that they KNOW what they’re doing is unethical and dangerous, but they’re doing it anyway because they think the ends justify the means.