In Star Trek, the Federation is a fleet of heavily-armed ships sailing out to tell everyone else what's moral. It works about as well as that ever does. We're told that they're the good guys, but that's because we've been watching hu-man propaganda. But no matter how bad the movies got, it was the various TV series which really showed that the Federation was an evil empire.
#5. Blatant Human Elitism
Starfleet serves the United Federation of Planets, and one planet is way more Federated than the others. Starfleet headquarters are on Earth, most of the Admirals are human, most of their captains are human -- even their flagships have only one token not-exactly-human-looking alien per bridge crew (and even then, only when they look pretty human). In our universe, we know that makeup is expensive and that actors are generally human-shaped. But in their universe, the effect is clear: The closer you are to perfect Homo Sapiens, the better the job you get.
"Bzzit-damn, but you look expensive. Don't get too used to the camera."
Starfleet doesn't hang street signs in space, but they named everything else after Earth, just to make sure nobody forgets who's in charge. Their starships are all named either for aspirational concepts or Earth locations, with the clear implication that those are equivalent. It's fine when you're naming a ship after a heroic cosmonaut, but by the time you're down to Terran rivers, all the other Federation species must be feeling the middle finger. Imagine Andorian scientists at the Utopia Planitia shipyards.
"We've built a new starship, and my homeworld's greatest explorer-scientist and peacekeeper would be would perfect ..."
"Don't get bluer balls, antenna-boy, we've still got a few cities we haven't used. Saratoga."
"Eat a large number of mid-sized American towns, Borg!"
Doctor McCoy demonstrates that constant anti-alien rhetoric is welcome at the higher levels. Earth is "Sector 001" while the other federation founding members are in sectors 005, 006, and 007. Humans invented warp drive, met entire alien worlds, and resurrected the geocentric model of the universe just to spite them. The worst offender (but best Star Trek series) is Deep Space 9. It's all about a Federation outpost to an entire quadrant whose name is incredibly insulting to the locals. They might has well have called it Starbase Arse End of Nowhere, But Only After Eight More Important Arses. That's gotta be rough on the Bajorans. "We live here, asshole. You guys even give your unmanned probes big fancy mythical names, don't you? And we're Faraway Numeral."
Bajoran nose-creases are caused by the constant stench of Federation bullshit.
#4. Starfleet Military Vessels Hoard Resources
The starship crews fly around like they're enjoying a post-scarcity utopia, but the fact is that the Enterprise has a gas tank. That big shiny warp core is just a reaction chamber. Annihilating a half-kilogram each of matter and antimatter releases two hundred billion percent more energy than a kilo of gasoline, but it's the exact same idea. The warp core isn't a magic energy source; it's an Internal Annihilation Engine. And it burns fuel. Which has to come from somewhere.
Deuterium gas guzzler
It's hilarious to note that the Enterprise was originally intended to use lithium, so that the starship of the future was just working on an immense battery. But here's the thing: It still is. The batteries are just antimatter storage pods. Don't even mention the backup fusion reactors, which are crumbs compared to the main power; a few thousandths of a percent compared to the 100 percent mass-energy conversion the ship is designed to use. The TNG Technical Manual mentions an "Antimatter generator," but it's an extraordinarily inefficient device designed only for emergency use. Fueling the ship with that would be more nonsensical than claiming the Enterprise-D is powered by a hamster running in a little wheel. And in the ship's official on-set Master Systems Display, that's exactly what they do.
Paramount, via via Joel Zink
The Enterprise is approximately 250 microHorsepower
This explains why a universe with replicators and holodecks isn't an infinite utopia, and why they keep meeting people who are struggling and starving. When replicators run off antimatter supplies, they're not infinite food, but an obscene luxury. That's how you can have a Klingon restaurant right next to a replicator on the DS9 promenade. Those who haven't signed up can't afford the fancy Federation machine. Eating whenever you want is a Starfleet signing bonus.
That's what the "Prime Directive" is really for. They're not shielding developing species from undue influence. That would mean not going near them at all, and definitely not repeatedly beaming down and having sex with the natives, like in several episodes. They're freeing themselves from the guilt of not helping thousands of underdeveloped worlds while squandering their limited supplies on immense military vessels. Speaking of those vessels ...
#3. Starfleet Is A Bunch Of Idealistic Suicide Bombers
Starfleet captains proclaim themselves peaceful ambassadors while standing on immense antimatter suicide bombs. Every Federation starship stores years' worth of the stuff in "antimatter storage pods." They make the Exxon Valdez look like a water balloon, and the Enterprise experiences terminal warp core breaches more often than it experiences same-sex relationships.
The White Steam of Death
In the original series, Kirk bluffed that his ship was made of "Corbomite," a fictional substance which would detonate and destroy pretty much everything if it was fired upon. He did this for two reasons: to analogize the Cold War, and because even he knew that no one would believe that all Federation starships are really beds bolted to the biggest bombs in existence.
Even if the antimatter pods are somehow safe -- and they'd have to be, or power-damping fields would be the most lethal first-strike weapons in the galaxy -- at any instant, the power system is filled with enough antimatter to at least explode engineering. The dilithium crystals preventing this depend on extremely high-frequency field emitters. This on a ship where the keyboards explode, and they they're not even filled with antimatter. They don't even have keys!
When you touch these pads, THEY TOUCH BACK
The littlest interruption to the dilithium system would set off a chain reaction that would kill everyone in the area. The first time the ship gets hit by an energy-dampening field, the bridge should suddenly go dark, then suddenly go bright 1.3 microseconds later, as the expanding gamma ray wave plasmafies everyone's retinas. And it doesn't matter what kind of magic antimatter storage pod you have; this would open them to the total annihilation of the entire supply, and the obliteration (or EMP-induced chain reaction) of every ship in the area. And the crews keep climbing into these deathtraps to spread their message to new worlds. No wonder everyone acts friendly to the Federation. So much as bending their fender could get everyone in the sector killed!