It strikes me that many people like to idolize Starfleet and the UFP (especially on Trek Twitter) but neither Starfleet or the UFP have ever *really* been shown in any show as being especially positive.
I mean, I think it's overstating things to claim that Starfleet and the UFP have
never been shown to be positive. The Federation has consistently been depicted as a state in which hunger, classism, racism, disease, patriarchy, religious bigotry, etc. -- essentially most forms of large-scale social inequality -- have been eliminated. Starfleet has consistently been depicted as working to advance Federation science and diplomacy. The UFP and Starfleet have always been depicted as embracing diversity and multiculturalism. Etc.
It would be more accurate to say that while broadly positive and representing huge progress over the systems that exist today, the Federation and Starfleet have never been depicted as perfect and still have systemic flaws that the people of the Federation must continue to work to overcome.
It's more than simply being at odds with our hero ships; here are just a few examples from memory:
The number of admirals/commodores who hop on board James Kirk's Enterprise to muck things up and force the captain to clean up the mess -- the Corbomite Maneuver for one.
I'm afraid you're misremembering "The Corbomite Maneuver;" that episode is about the
Enterprise encountering the
Fesarius, a vessel of the First Federation piloted by Balok. Balok is at first wary of the
Enterprise and threatens to destroy it, but he relents and forges a peaceful relationship once Kirk proves the Federation's benevolent intentions to him. No admirals are present in the episode.
It
is true that sometimes admirals or other higher-ups have conflicts with Kirk. Sometimes, those conflicts are indicative of a fundamental corruption of the admiral, but most of those conflicts are just differences of command judgment that would be present in any society. It's not indicative of some systemic flaw with the Federation.
The UFP in Kirk's era seems to have a large number of mining colonies of dubious condition. Unless we assume that the miners of Mudd's Women and Devil in the Dark were working the mines for their own betterment and enjoyment. Granted, the UFP may not be directly responsible for the mines, but it does make one question the system that would still allow the mines to be operated in the manner in which they are shown.
It is true that the dilithium mining industry in the 2260s appears to be characterized by extreme hardship and isolation. "The Devil in the Dark" makes it clear that the industry's workers are often at least in part motivated by a desire to achieve great wealth, so clearly the Federation is not a society in which there is no commerce. "Mudd's Women" strongly implies that there is an associated sex worker industry built up around miners' demands for companionship, and possibly a sentients trafficking industry as well. One would hope that in an enlightened society, consensual sex work is legal and well-regulated so as to avoid sentients trafficking and associated sentient rights abuses.
"The Devil in the Dark," however, strongly implies that cooperation with the Horta will revolutionize the mining industry. I find myself wondering if the advent of Horta mining might have led the humanoid mining industry to essentially end?
The entire subplot that Starfleet admiralty knows that Spock or at least his body may be on the Genesis planet but won't allow Kirk to return to the planet in spite of the fact that Spock is both a high ranking Starfleet officer and the son of a super influential Vulcan ambassador. They won't help Kirk or Sarek simply because Starfleet Command doesn't understand Vulcan mysticism.
I think it's clear Starfleet made the wrong call there, but their caution was understandable. The Genesis Planet was an unanticipated development of the Genesis Device being used in a manner for which it was not designed, and all this happened without Starfleet knowing about David Marcus's use of protomatter, and in the context of the Klingon Empire and God knows how many other interstellar neighbors feeling incredibly paranoid about the potential of the Genesis Device to serve as a powerful, genocidal first-strike weapon that could wipe out all life on their planets with almost no warning.
The UFP is willing to hand over a number of worlds colonized by its own citizens to the Cardassians for the sake of a treaty. The colonists basically get a "Oh, your homes are here? Not anymore, buddy!"
I think that's an example of a situation where there will always be conflicts between the best interests of a larger polity and the best interests of a smaller community. What's the alternative for the Federation -- war with the Cardassians that could kill hundreds of billions of people? On the other hand, why should those Federation settlers have to give up their homes just because of Cardassian imperialism?
I don't think either side is truly wrong there.
Not only does the UFP pull eminent domain, but they essentially rescind citizenship
I think you are misremembering the situation. The Native American settlers on Dorvan V are the only Federation citizens whom we know canonically lost their UFP citizenship, and they renounced their citizenship of their own choice so as to stay on Dorvan V in compliance with the treaty. They willingly subjected themselves to the authority of the Cardassian Union.
and protection for anyone who chooses to stay on those plants and ultimately treats them as terrorists when they fight to stay in their homes!
Relinquishing the right to protect UFP citizens who stay on worlds ceded to the Cardassians is a necessity of the treaty, but yes, the UFP also absolutely did not do enough to protect those Federation settlers who remained on UFP worlds in the DMZ who were being attacked by Cardassian militia groups that were secretly armed by the Cardassian government. And Michael Eddington's critique of why the UFP reacted so badly to the Maquis when it became clear that their ultimate goal was to secede from the UFP and establish their own independent state in the DMZ is completely fair: "Nobody leaves Paradise! Everyone is supposed to
want to be in the Federation!"
The forced resettlement of the Baku was approved by the Federation until Picard essentially forced their hands to reconsider.
Yes, although I do wonder if Admiral Dougherty described the situation accurately when he got the Federation Council's approval. They were
so quick to side with Picard that it make me wonder, especially since, quite frankly, it would not have been particularly hard to just send in another ship and place Picard and his crew under arrest.
These are just a few moments that popped into my head that are way worse than Starfleet not helping the Romulans
I fundamentally disagree here. Allowing tens of billions to die in an act of apathy is far, far worse than any of those examples you just cited. It was fundamentally depraved.