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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.
Angst? What Angst?: Dietrich. While justified, it can be a little jarring to see how (apart from his event in Gunnitz) very little mention about his brother doesn't seem to bother him at all, almost to the point they are complete strangers.
Cliché Storm: Abso-freaking-lutely, especially with regards to characterization.
Crowning Music of Awesome: Most of Act 2 map theme, the regular battle theme, and the track that plays when your ship docks on normal occasion.
After the battle against Orders in Act 2, Roth cries over his damaged-beyond-repair ship in such childish manner. This will remain funny if you recruit Katida, but if you don't, cue the final battle against Lugovalos, where Roth (already badly injured) overloads his ship's high-stream blaster to defeat Katida, guaranteeing his ship will be destroyed for sure.
An event that allows Princess Glorinda to be recruited has PM Falko asks Yuri if he has "special someone", in which if Yuri answered "yes", Torlo will (perhaps jokingly) states that his "special someone" is Kira. Later after the battle against Lugovalos is over, Torlo and Tatiana tell Yuri that he should find a girlfriend, and their suggestion? Glorinda. Granted, Yuri is the only one who remembers Kira, but considering what happened, it's really harsh.
You may think it's Valantin's Corsair, but no. The Absoluta is hands-down the most powerful ship in the game. It boosts both your accurcy and evasion by an insane amount, meaning: You practically won't get hit ever while you can even hit enemies in the backrow consistently. Using the Absoluta as your flagship makes the rest of the game almost trivially easy.
Fighters fit a stricter definition of this trope, in that they're a "nuke" option in the Tactical Rock-Paper-Scissors. They're more effective against enemy ships than ship-mounted guns, and they're also more effective against enemy fighters than anti-air guns. In addition, once they start attacking an enemy, that enemy is held in place, allowing you to choose the range of the battle, and that can include retreating beyond their gun range and letting the fighters kill all of the enemy. In other words, "throw fighters at it" is always a superior option to any tactic that does not include "throw fighters at it."
One of the first clues you can get regarding what happened in the Irvest sector is that the speed of light has changed in the area. Or, in physics terms, Irvest Sector has just gotten bigger.
Goddamned Bats: Almost anything you fight before you gain access to ships those will match the enemies, even in New Game+. The LMC pirate ships (Sodality, Junkyard, and Fellowship) are the most notable examples, since they're fast and have high durability compared to your SMC ships. They are also not very worth fighting since the reward is so small (except when they appear along with Hestia, which will drop a large sum of money), so it's usually better just to run away.
Hell Is That Noise: The screams you hear upon entering the Flux Sector for the first time.
Ho Yay: Cico is just a little too... obsessed with Yuri. Dietrich is also really fond of him.
Magnificent Bastard: Valantin. Sure, he pinches your dad's Epitaph and stabs out your eye when you first meet, but it's hard to hate him. Him not being a villain does not help.
Nightmare Fuel: Flux Space, Desmond Gate, Rubriko's clones, the Phages... plenty of stuffs in this game can be disturbing, actually.
If fighting Mikelo five times isn't enough to freak you out, then watching how his spare bodies suddenly come to life while screaming and such before all of them fall to the ground should do.
The artificial Epitaph that Professor Minas created caused Trevor to merge with the Dead Gate nearby, turning said gate into some sort of primitive life force that will attack anything nearby.
Player Punch: Everything that isn't epic or funny in the game. The best example is when you just fought your way through a bunch of pirates and had to go through a dense meteorite storm to rescue a hostage that seems to be a new crew member. You get to her and when you move her out of her cell you realize too late that she was rigged with explosives. And she wasn't dead.
She doesn't have to die if you decide to execute Argun, but she won't join your crew anyway.
Franny is probably the most obvious example, as she is generally hated for annoying personality and low stats.
Katida. Some players dislike her personality, some others hate her after all of the troubles to recruit her, she doesn't have any story importance whatsoever other than to avoid Roth and Nele from being killed.
That One Boss: Several, although it also depends on the player. Taurus Fortress is generally agreed as one due to the massive damage it can cause.
They Wasted a Perfectly Good Plot: One of your missions involves defusing a dispute over resources. Coulda been, you end up picking sides, or been one of the captains on either side. Nope. Wonderboy and Obi-wan get it fixed.
Of course, this basic plot does happen at least two other times, down to picking sides.
To add to that, Katida, for all the trouble you go through to recruit, doesn't get any sort of story (save for a minor event between Kira and her) in the second half of the game other than you rescuing her and becoming a permanent part of your crew. Although to be fair, having Katida in your party will prevent the Mummies at the Dinner Table above from happening.
Arguably, how several plot-important characters' past (particularly Nia) are never brought up at all falls into this trope.
No, people, we wouldn't actually travel the Magellanic Stream. Which was hyped up as the most dangerous route in the universe and nigh-impassable.