Badass Gay: most of the queer characters, as this is a story about superheroes.
Beast and Beauty: Lazarus and Tomo, although calling Tomo a "beauty" is pushing it. (She does fit the trope by being more conventionally attractive than he is, and compared to some of Laz's other associates, Tomo's a good influence.)
Speedsters, anyone with physically-based (as opposed to telekinetic) flight, anyone with Healing Factor, and many energy projectors have particularly high caloric needs if they use their powers heavily.
Bizarre Human Biology: some mutants, most commonly those with physical power sets. Sometimes (as with Aria Limax), the weirdness is the power.
Atlanteans would also count, as despite their adaption to aquatic life, they're still genetically compatible with baseline humans.
Blind and the Beast: Lazarus (implied to be horribly disfigured under all the gratuitous bandage wrappings) has an off and on relationship with Tomo. She knows that he's not "normal looking" but doesn't care.
Cut Lex Luthor a Check: averted with Victoria. She's perfectly capable of making money legitimately with her scientific talents (at least when being a wanted terrorist doesn't interfere with dealing with patents and marketing), and views her supervillainy as a form of activism, not a day job.
Cute Little Fangs: most of the Lilim, and not uncommon among other mutants with visible mutations.
Cute Monster Girl: most mutants whose mutations dramatically effect their physical appearance. Even the ones who aren't conventionally pretty have a certain offbeat charm.
Dark Age of Supernames: single-word aliases are normally the rule, but they don't normally get into grimdark territory (with the possible exception of Necromancer and Nightshade.)
Dysfunction Junction: any group of supervillains. Prodigium may be one of the most functional, and they have to deal with Elisa's emotional problems, Fernando's survivor's guilt and revenge obsession, and Victoria's (wo)manpain and occasional megalomania.
Elemental Baggage: for kineticists, whether this trope applies depends on what they're manipulating. Materials manipulators need a source of raw material, energy manipulators can create their own if necessary but usually need to burn a lot of calories.
Lebensborn averts this. The upper ranks consist almost entirely of able-bodied white people.
Esperanto: is one of the official languages of the Republic of San Alberto (along with English, Albertan Creole, and Atlantean.) A few influential members of the founding government were Esperantists, and when you have to print all official material in three languages already, adding a fourth isn't too hard.
Everyone Went to School Together: whether you're a middle-class girl studying child development, a scholarship student studying biology, or a genius heiress studying engineering, Northwestern Polygnostic University is the place to go.
Ghostapo: the creepy occultist-Mad Scientist lady who turned Michael Mendelssohn into Iron Seraph. Whether or not she actually subscribed to Nazi ideology, she certainly had connections with the regime, and had no compunctions about picking up test subjects at concentration camps.
The Good, the Bad, and the Evil: various heroes as the Good, Victoria and her followers as the Bad, and Lebensborn, the Hand of Ares, and various anti-mutant hate groups as the Evil.
Galatea Xiao as well, in a more hands-off sort of way.
Nightshade as well.
Any petite female character with a physical disability is probably going to be able to end you.
Hatedom: The Alchemist, in-universe, as sort of a counterpoint to her (unwanted) worshipers. It's split between those who think she needs to stop throwing her weight around and let regular people run their own lives, and those who think she's a lazy neglectful slackass for not helping out as much as she theoretically could.
Horny Scientist: the director of Canada's Cold War era Super Soldier project had a thing for Cat Girls and Action Girls. This may have had something to do with why the program kept an interest in Tomo Kojima and Lucy Fraser as long as they did, despite the former's blindness and the latter's cheerful psychopathy.
A Nazi by Any Other Name: Lebensborn, although with the eugenicist/"purify the Master Race" aspect emphasized more than the racism. (In other words, they're more hostile to mutants with "sub-par" powers than to genotypical humans who aren't currently standing in their way.)
Power Nullifier: a few martial artists (notably Daemonette) can temporarily disable some superhuman (mutant or otherwise) powers by hitting Pressure Points. Efforts by various Sinister Secret Agencies™ to turn this into a permanent depowering process have failed, but there has been some progress in treating Power Incontinence with glorified acupressure bracelets.
Prehistoric Monster: averted. None of the species Victoria recreates are dangerous to humans (because Victoria, for all her Mad Scientist tendencies, wouldn't make something she considered likely to eat her), and some of them, like Archie, are sort of cute.
Lazarus is sometimes referred to as such, but he is capable of meaningful emotional attachments and, on occasion, remorse. He's just impulsive, "morally confused," and uncomfortably comfortable with violence.
Spirit World: the Astral Realms, which are oddly like a psychically-accessible version of Second Life, with less loading and porn.
Spot of Tea: many characters. It is apparently the Helix Universe's official hot beverage.
Spy Drama: many of Loki's adventures. Stale Beer-flavored in terms of the level of cynicism, but served in a martini glass, with a twist of lime and a shot of absinthe.
When other major characters get in on the action, the tone is generally mildly hallucinogenic Dirty Martini.
Squishy Wizard: most telepaths, compared to other mutants and DPIs. They're not necessarily any squishier than a baseline genotypical human, but telepaths' Required Secondary Powers don't normally give them any additional physical resiliency, telepathy is useless at blocking most kinds of physical damage, and mind-reading isn't very good exercise.
Superpower Lottery: the Alchemist can control matter at an atomic level (the source of her name), as well as teleport, completely control her physical form, slow down or speed up her perception of time, and survive in a vacuum. She's capable of turning the world's nuclear arsenal into cotton candy. (And has.)
On a slightly more down to earth level, Galatea Xiao and Victoria Paracelsus. Grimoire has the potential, particularly if she ever learns to make constructs from scratch.
Time Travel: involved in Kensei's backstory, and is responsible for Valkyrie II's alternate timeline.
Tomboy and Girly Girl: Tomo and Shoshi, respectively. Although Tomo and almost any other woman in the cast with whom she has significant interactions could count.
Among the students at the Academy, fraternal twins Swift (super-speedster athlete) and Grimoire (psychic bookworm).
Touched by Vorlons: many non-mutant supers got their abilities through contact with some kind of powerful mystical being or alien.
Trans Equals Gay: Victoria ran afoul of this assumption when she was young, and her dad saw his "son"'s feminine tendencies as the reason to make a Cure Your Gays attempt. Never mind that Victoria's never actually been romantically interested in guys.
Ugly Cute: in-universe, this trope winds up biting Concerned Citizens for Genetic Purity in the ass. Their slideshow of visibly mutated children (intended as a "this is what your grandkids could look like if the mutant threat isn't contained" scare tactic) sets their audience awwwing instead.
Unfortunate Implications: in-universe, merfolk, therianthropes, and superpowered mutant humans are real, which creates some potentially problematic aspects to certain speculative fiction tropes that aren't an issue in our universe.
Unusually Uninteresting Sight: Shoshi, Khadijah, and Emmanuelle might attract attention from people who aren't used to them, but people seem surprisingly blase about Lazarus running around in a full-body ninja mummy outfit and carrying a dojo's worth of pointy objects.
Unwanted False Faith: there is a small cult that worships the Alchemist, with no encouragement from her.