As for the concept of Section 31 itself, honestly it's quite absurd when you really break it down. The reason why it worked so well in DS9 was because you never knew if it was an actual thing, or if Sloan was just trying to fuck with everyone. But once they decided, yes, it was a thing, then it just became a silly trope and has gotten worse with each new iteration.
Even in DS9 it gets ridiculous very quickly. It starts out as counterintelligence/internal security, then foreign political operation, then some kind of WMD skunkworks (which it would have had to have been before it was the other things given the timeline of Odo’s infection). These are all very different things without a lot of transferrable expertise! I’ve seen people lament how Trek’s lost any knowledge of how a military organization actually works, but they’ve
never been good with intelligence.
It’s not usually an issue because Trek isn’t usually focused on that, but it’s bad because Trek usually falls back on clichés—not just Trek clichés but genre clichés and Hollywood clichés in general—and calls it a day, while a better understanding of intelligence probably would result in richer storytelling rather than more limited storytelling.
Plus there’s something really juvenile about having a “bad stuff” division. Lots of intelligence work doesn’t even register as unethical. Few people actually thinks about their job that way. When we get into unpleasant choices it’s often because there’s a worthwhile trade-off, which is the subject of a lot of good drama. Often things go wrong because of broader institutional failure rather than outright evil, which is also good drama but means you have to write people working for an institution which is just not how current genre writers seem to think (you’re either a lone wolf or a part of a small band of superheroes/rebels/outcasts who live in a world that’s an extension of their inner emotional life, not someone working in an organization with larger goals that intersect with your own).
Edit: So I guess my head canon as far as §31 is concerned is that the DS9 incarnation is really a relatively small “meeting group” of a few people in parts of Starfleet and the Federation’s security apparatus, plus a few veterans operating outside, who use their influence to head towards a set of common goals, but nothing official (but tolerated due to the paranoia and strain of the Dominion War) and most of their capabilities come from misallocating legitimately-appropriated resources. Maybe it’s named after a 22nd-century agency, but there’s no continuous history and there’s no way it stays secret for long, probably collapsing over its own weight after the Dominion War (I’d bet it’s like the “Conspiracy” parasites, where we follow our main crew but, per “The Drumhead,” other people are also on the trail off-screen). There’s no way it stays secret for centuries, particularly if it’s a large concern. I’m not certainly going to be rewatching or watching other stuff involving §31 so I’m not really worried about reconciling my headcanon with actual canon here.
