I have been told that DS9 isn't really a true Star Trek but is a kind of plagiaristic copy of Babylon 5. I don't really care if it was because I enjoy both of those shows.
While most of the evidence suggests that's true, you're right that they're still really good shows and I loved how the writers were willing to push the boat out more with DS9, instead of sticking to the same tired old formula and made Voyager and Enterprise a slog to sit through at times.
I've only recently started watching B5 and I can definitely see the DS9 parallels, although given how much B5 would go onto inspire and be homages in the Mass Effect series, it's harder not to think of ME than DS9 nowadays.
Except at driving the Enterprise... 
Poor Marina Sirtis, the only time Troi ever got to pilot and both times she ended up crashing the Enterprise D and E into something else! Blind guys, Klingons, Robots and teenagers all managed to pilot that thing for years without any hassle, but put her in the chair for two minutes and one ship ended up totalled and the other suffered a major fender-bender (although that last one was deliberate).

As for the original topic...
I've always taken that the Federation is a False Utopia masquerading as as perfect society, using a form of benevolent alien invasion to basically seize dominion over the galaxy inch by inch?
Sure, they're nice and they offer all these nice things, but you have to trade in your unique culture, clothing and ship designs and instead adhere to Starfleet principles, wear the same godawful uniforms with a strict dress-code and little leeway to cultural items (sure, Worf wears a klingon baldric, but Ro and other Bajorans can't wear their earrings) and use the same dull, grey ships the Federation uses.
All this suggests that the Federation deeply values conformity, even if they claim otherwise, because if you tell people exactly how they are permitted to think, dress and act, then there's no longer and disagreements between people? No wonder they somehow stamped out war on Earth, if they're group-thinking people from birth not to go against the herd? Eddington might have been a jerk, but he wasn't wrong in pointing out that like the Borg, the Federation loves to assimilate people without them even noticing.
As a final note, given the sheer lack of any LGBT representation in over 50 years of Star Trek, it honestly makes me wonder whether not that Earth has simply decided to shove everyone back in the closet, and how many Krem's and Dorian's might be currently living in the Federation?