some trope removal/edit suggestions:
probably remove: Anachronisms, By Royal Command (obv they do meet alien rulers but it’s not really the same), Days of Future Past and Days of Present Past (there are stories that would fall under these but again it’s just not the same imo), Evil Toys (TNG’s The Game might fall under this?), Factory, Influencers, News Report, Profiting from time travel, Romans, Time Agent, Time Eddy, Vikings
maybe remove: All Aboard! (not enough trains in Trek, alas), Capitalism is bad (this is just the Ferengi), Controlling the Beast (I can’t think of any instances of this), Dear Diary (or maybe rename to Personal Log for that Star Trek vibe? idk), Dinosaurs (there are dinosaur stories but are there enough?), Everybody Dies (too many core cast members for “everybody” to pack the same punch. also not sure it happens that often), Everybody Lives! (same sort of reason), Human Traitor, Life force, Living Art, Monster Origin Story (I can think of at least one thing that would fall under this but idk. Trek doesn’t really do monsters the same way Who does), New Old Friend, On the Beach (do they go to the beach ever?), Reality TV (I can think of one story that would qualify for this), Halloween (there are a few but generally Trek doesn’t have that much holiday stuff & there’s a big overlap with Spooky anyway), Post apocalyptic, Stone Circle, Time Travel Pivotal (doesn’t make as much sense in a setting without regular time travel), some amount of Tourist Attraction/its subtropes, Virtual Reality (substantial overlap with holodeck, although there are some non-holodeck VR stories), Tombs
definitely remove: Deadlock Seal, Earth Invasion, Edge of the Universe (maybe replace with Edge of the Galaxy?), End of the Universe, Fake Regeneration, Frost Fair, Mysterious planet Earth, Non-interference policy (covered by Prime Directive), World War I, World War II
other suggestions: edit the Faulty Translation description to just be in-story since i.e. Klingon goes untranslated all the time. take out the ‘past lives’ bit in the description of Flashbacks. Rename “Held at Gunpoint” to “Phaserpoint” maybe? although that sounds silly. Also in general there are a lot of trope descriptions that reference the Doctor.
Are “Badmiral” and “Only ship in range” meant to be subtropes of Prime Directive? That seems odd.