On the other hand, I'm left wondering how many times we're really talking about. In the TOS era, for instance, certainly Starfleet contained a few commodores and admirals whose sense of their own importance might have been a bit inflated, and a captain or two who went off the reservation, but I don't recall anyone who actually betrayed or undermined Starfleet and/or the UFP. That didn't happen until STVI:TUC. Then in the TNG era, there was the conspiracy in "Conspiracy" (but that was actually alien parasites) and later "The Pegasus," in which an admiral had conspired with Starfleet Intelligence to violate a treaty agreement. In DS9 we got "Paradise Lost," in which an admiral conspired to commit a coup, and eventually "The Dogs of War," in which the Federation Council tacitly endorses Section 31's plan for genocide against the Changelings.
But unless I'm forgetting something, that's about it. (Setting aside the events of STID — gakk, thankfully an alternate universe! — and Treklit novels like, e.g., Dreadnought). By comparison with the level of dirty dealings conducted by the US government and military over the last few decades, it actually seems like a pretty clean record. Perhaps our impression of the Federation and Starfleet's shortcomings is exaggerated?
Ah, yeah, I'd forgotten about Nechayev's plans for Hugh, Kennelly's analogue to the Iran/Contra deal, and Dougherty's plot in Resurrection.
Seems like most of the Starfleet corruption centers on the TNG era, doesn't it?
Perhaps that's just an artifact of having more episodes overall, or perhaps it really does make a difference that TOS was written in the pre-Watergate, pre-Reagan years...
Any way you slice it, though, I think Section 31 takes things to another level. The notion that there's an established organization devoted to black ops suggests something more systematic than just an occasional corrupt flag officer or politician, and the notion that the UFP would countenance or even support such an organization is even more disquieting. Insofar as S31 exists, I prefer to think of it as a entirely rogue operation — not unlike how it was originally introduced.
I think that "Federation = evil Admirals" is something which comes mostly from DS9, because they went way too far with it (and thus were shunned in this regard by the producers of the other series). Like they did with their whole WWII-in-Space way of handling interstellar conflict. If you look at it through the more optimistic lense of other series, and ignore the parts of DS9 where it was portrayed as a much deeper rot (Section 31, Paradise Lost), you actually get a much more optimistic picture:
- The Undiscovered Country is the only true example - and that's at a turning point of the Federation, where even the hardliners weren't "truly" evil, but wanted to protect their version of the Federation from what they thought were purely evil klingons.. And it was one(!) Admiral. Others (even Kirk!) shared the same opinion - but wouldn't actually act in such a non-legal way
- "Pegasus", Nechayef's plan for the Borg, and "Insurrection" are clasic morality plays, where in each case you will find many people agreeing with the Admiral - in each case a means vs. outcome argument, where the means were the problem, but the outcome would clearly be beneficial (contrast to DS9, where even the "outcome" would be either a military dictatorship, genocide on "real" natural beings (and not assimilated cyborgs), or the existence of a clandestine organization beyond the laws). I'm still not on Picard's side in "Insurrection". Dougherty is only wrong because he went the asshole way of handling things.
- And Kennelly (much like the Captain in TNG's "The Wounded") were clearly "bad apples" in a good organization that needed to be stopped the exact moment they went off the rails - e.g. an example of where the organization actually worked, and the bad apples needed to be sorted out immediately.