These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Trent (after you accept one of the final missions): Sure. As long as I'm not shot at, knocked out, held at gunpoint, electrocuted, skewered alive by giant alien shapeshifters, have to dive out windows or fight off spindly Nomad incubi...everything should be fine.
"Good job, but you're not done yet. There are more hostiles at the next waypoint."
"We read that your primary target's not there. Hold off his cronies until we can locate him."
Love It or Hate It: The control scheme. Keyboard-and-mouse users love it, while joystick users who can't use their preferred controls like every other space sim consider it a deplorable Scrappy Mechanic that ruined the game and possibly the whole genre.
For that matter, just suggesting the addition of a Freelancer-style control scheme in any other space sim community is a great way to start a Flame War.
Mary Tzu: Casper Orillion managed to steal an entire battle cruiser, among other things.
Nightmare Fuel: During the Liberty section of the game, most solars (planets or space stations) are green (friendly) to you, and red is reserved for enemy fighters. Then, when Trent and Juni make their escape from Manhattan, everything save for Juni's fighter is red. Including the Newark Station, Trenton Outpost, the trade lanes, and Planet Manhattan itself. What was once the safest place in the universe for you is now the most dangerous.
The Edge worlds are as far as one can go from civilization and reside within a Sickly Green Nebula, which makes it a creepy part of Sirius to begin with. Then comes the knowledge of Nomad presence in the area and that their homeworld is not far away.
Shipping: Done in fanfiction as a reaction to the lack of romance between Trent and Juni.
Stop Helping Me!: Allied ships have a tendency to fly into your sights during a heated battle, hence causing several unnecessary friendly fire incidents that can turn them, as well as their allies, against you if they are hit hard enough. This is more common in Liberty space, especially in the New York System, where most NPC fighters cannot survive more than three hits from the most powerful weapons in the game.
Straw Feminists: Zigzagged with the Golden Chrysanthemums. On the one hand, they are an all-female organization whose stated intention is to overthrow the current Kusari government and establish a matriarchy. On the other hand, they maintain a very close relationship with the masculine Blood Dragons. It's unclear whether this is just a long-running Enemy Mine setup or a true alliance.
Anticlimax Boss: The bombing run on the Nomad city is almost the same as the rest of the "blow up the shield generators" you are given every other mission.