I'll admit, it probably only seems like it is getting worse each time, than it actually was.
Especially when you compare the later series to TNG. It's like with each new series or movie, they crank up the dysfunction level.
An admiral tries to take over earth.
Well, technically, he was trying to take over the entire Federation, not just Earth. But Admiral Leyton is in essence the same sort of character as Admiral Satie from "The Drumhead;" he just got further in his authoritarianism before being stopped.
But he
was stopped, let's remember.
The Feds want to forcefully remove a peaceful colony while allied with a questionable power..
You mean like they did in TNG's "Journey's End?"
..The Fed tricked another power into going to war.
True, this is much darker than anything we ever saw in DS9. By the same token, though, the situation we saw in DS9 was much more dire than anything we ever saw in TNG.
The Federation did not attempt genocide; Section 31 did, without the Federation government's knowledge or approval. The Federation should no more be blamed for Section 31's genocide attempt than the Kingdom of Saudi Arabia should be blamed for al Qaeda's actions on 9/11, or than the Italian Republic should be blamed for the crimes of the Sicilian Mafia.
While it's true that that's darker than anything we ever saw on TNG, I don't see how that's applicable to the question of how the Federation was depicted. ENT took place before the Federation was founded; you might as well condemn the United States for the Kingdom of England's oppression of the Irish if you want to hold Archer's actions against the Federation.
I would suggest that the most basic reason we saw something so dark in ENT was that ENT's third season was being written in part as a reaction to the incredibly dark times it was written in. When "Broken Bow" first aired, smoke was still rising from Ground Zero in New York City. When "The Expanse" first aired at the end of ENT Season Two, kicking off the Xindi arc, the United States was only two months into an illegal war of aggression against, and brutal occupation of, the Republic of Iraq. I would suggest that it's simply not reasonable to suggest the STAR TREK writers of the 2000s should not have been influenced by the dark history unfolding around them is unreasonable.
And while it's true that Archer does some really awful things during the Xindi arc, it's also true that Archer's ultimate solution to the Xindi crisis is non-militaristic. Instead of seeking blind revenge against all of Xindi society for their attack on Earth--and attack that cost 7 million lives--Archer seeks to make peace. He seeks to persuade the Xindi Council that Earth does not represent a threat to them, and to help them realize they are being manipulated by the Sphere Builders. And he even teams up with some Xindi factions when the Xindi Reptilians refuse to believe that peace is possible with Earth. That's a far cry from the sort of blind militarism that has characterized much of American politics since 9/11.
It's like the only thing about Utopia that remained stable is the prosperity and that's it.
Again, the Federation was never utopia. It's always had bad apples, and it's always had some institutional injustices that require Our Heroes to stand up against. And that's fine, because all governments are and will always be vulnerable to institutional corruption; we can never be delivered from history. STAR TREK does us, the audience, a disservice if it ever implies there will one day be a governmental system that will be immune to the temptations of power; STAR TREK's optimism doesn't come from the idea that there will never be corruption and injustice, but from the idea that a vigilant populace and vanguard will stop it. STAR TREK isn't optimistic if Admiral Leyton never tries to launch a coup, it's optimistic because Captain Sisko stops him.
What it boils down to was either Picard full of it, telling the truth, or in denial of what the Fed really is.
I think it's safe to say that the characters in early TNG tended to overstate the Federation's virtues, and to overestimate their own levels of enlightenment. I think it's also safe t say that the Federation's flaws do not render it some sort of horrible, monstrous regime; it is, by any reasonable measure, a far more free and far more egalitarian and far less oppressive society than any which exists in real life.
Or was Utopia, as desirable as it is, was too boring to do for long, and they had to make Trek more edgier?
It's not that utopia is boring. It's that it's dishonest. It can never and will never exist. It's not optimism to imagine perfection, it's optimism to imagine progress.