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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.
YMMV: On the Shoulders of Giants
Crazy Awesome: Teddy, the AI that believes that he's Teddy Roosevelt, led a cavalry charge against Berserker ground forces, while standing on a tank in his humanoid avatar/platform and wielding a saber.
Hilarious in Hindsight: The timeline mentions that in this universe, thanks to a particle accelerator that encircles the moon, they discovered the Higgs Boson particle in 2087... when evidence of its existence was found in the real world in 2014. Whoops.
Iron Woobie: Petan. The guy's a huge, heavily armed and very badass combat craft, with a history that makes you wish it was physically possible to give him a hug.
Well, he recently got a robotic body, so you can now give him a hug. How he reacts to that however...
Uncanny Valley: The general consensus of the fandom is that humanity will feel this way towards the various humanoid races of the council after having experienced such a massive variety of alien types. In fact, some on the forums speculate that the races that humans (and the other Local Group races (SAC and the CDC)) will feel most comfortable with are the Hanar and the Elcor, the only two races that aren't humanoid.
Averted, the contact appears to have gone off well. Although everyone still finds Edani to be scary.
Interestingly, the AI's that use human-shaped bodies get more of this from the Citadel, but not because they look different... but because the Citadel is familiar with infiltrator-style robots, and they've had them used against them before.
Woobie Species: The quetzal. Humanity found three hundred and twenty six of them in suspended animation on Titan, where they'd been for three thousand years after being attacked by an unknown ship (later discovered to be a Berserker). A later mission to their homeworld found that it had been devastated by the Berserkers about three thousand years ago, with all life being wiped out, making the quetzal found on Titan the only surviving members of their species. While humanity has treated them well, the quetzal live with the knowledge that they owe them for pretty much everything, from rescuing them from Titan to giving them a home on one of their space habitats, and consequently feel that they owe humanity a debt that can never be repaid, not to mention that it is heavily implied that what remains of their culture will eventually die out due to successive generations of their children growing up surrounded by human culture.