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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.
Author Tract: The lead developer for most of the line's run was a gay man with issues, most of which showed up very heavy-handedly in the background materials. Expect any gay character to be in some way uber-powerful and/or infallible. Conversely, any conservative/hetero-normative types will inevitably be some breed of foolish bigot who will eventually get shown up... hard.
Although, in game canon, the "paranoid" anti-Nova types are right about the threat the Novas pose, and they just happen to overlap with political conservatives.
Of course, when the potential threat turned into the actual threat because of the actions taken by the anti-Nova types as precautions against the potential threat, things become somewhat less cut-and-dried. Just the nova sterilization conspiracy alone... that one makes no logical sense as a means of preventing the Aberrant War, because it is a blatantly warlike act in and of itself. (Specifically, biological warfare. That's exactly what it is. In all truth, the Aberrant War technically begins in 1998 the instant Aeon starts working on mass nova sterilization; it just didn't reach an open war stage until 2049.) It does, however, make perfect sense as an attempt to win the Aberrant War, via pre-emptive sneak attack. So, yes, Proteus was created to try and avert Mercer's future glimpse of the Aberrant War... but Proteus was the Self-Fulfilling Prophecy that led to that war instead.
Canon Sue / Villain Sue: Divis Mal, so much. He's like Magneto, but he's canonically right, he's on an entire different power tier compared to most of the setting, he has the ability to depower or empower other supers at will, and basically the entire plot is caused by and guided by him, with the players having no capability to effectively disrupt his goals, let alone attack him effectively. At one point, supposedly, one of the developers said that the title of the game, Aberrant, referred to Divis Mal specifically.
Pretty much any gay male character is destined to be a Sue of some sort and any other type of LGBT character comes close behind.