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.
Genius Bonus: Tsugumi's associated ride is the Jellyfish Gondola. There's a certain species of jellyfish that is biologically immortal due to the ability to continually transition between its larval and adult forms, effectively giving it eternal youth. This is similar to Tsugumi's own circumstances as The Ageless.
To be more specific, while it's still very popular in Japan, it's just one out of many different Visual Novels, and so has pretty much found its own niche. In other countries, where very few Visual Novels are translated, it's considered a classic and one of the greatest Visual Novels of all time.
Fanon Discontinuity: Sora's route sometimes gets this treatment, as players almost universally agree on it being the worst part of the game.
There's also You's fortune telling to Takeshi, where she predicts a variety of things about Takeshi's future. By the end of the game, at least half of her prediction comes true.
One of Kid's arguments to You why he doesn't need to know his name is that dolphins are intelligent yet don't have names for each other. Actually...
Inferred Holocaust: Sora's ending seems to imply that everyone except Tsugumi would die of Tief Blau, since no one was injected with the vaccine. They would probably infect everyone in the rescuing party as well, leading to the epidemy being that bit worse. Tsugumi herself would probably end up in the hands of Leiblich, and so she and her children would be in for endless torture and experimentation, without even death to spare them. But it's still supposedly a "good" ending.
Even in the True Ending, Tsugumi, Takeshi and You will have to watch their children grow old and die while they stay young forever. Well, maybe not You'aki, as she could still be exposed to Cure, but Hokuto and Sara are specifically stated to be immune to Cure and its life-extending effects.
Also apparent when Kid walks in on You and Sara cuddled together sleeping, and You being particularly possessive of Sara's body in their half-asleep state. Slightly subverted in that Kid contemplates on squeezing in between the two, if only he was sleepy.
And again in You's route, while not quite obvious; Sara realizes Kid and You's relationship and tells Kid she's jealous, but because it's him, she'll let it go.
In the remake, this becomes a Running Gag: Sara and You frequently act out dialogue similar to cliché Schoolgirl Lesbians at a boarding school (speaking to each other very tenderly, mind you) in order to tease Kid, and at the end, just when it looks like they're going to take it to the next level, they break off and laugh, usually leaving Kid blushing.
Memetic Mutation: "Why is she in a washing machine?", referring to Tsugumi in the submarine.
Rescued from the Scrappy Heap: While not exactly a Scrappy, Kaburaki was fairly unremarkable in the original game. The remake fixes this up by giving him a lot more Character Development and personality, an actual backstory, and a much closer relationship with Takeshi.
None of those compare to how they portray Hollywood Hacking. It involves duplicates of Sora battling each other with one Sora trying to buy time for the protagonists.
Hokuto somehow projecting himself into the past, resurrecting Takeshi through The Power of Love, and then gushing over him and repeatedly calling him "dad" throughout the entire rest of the ending can easily fall under Narm or Narm Charm depending on the player.
The Woobie: Almost all of the characters count, but especially Tsugumi and Yubiseiharukana.
Woolseyism: In the Japanese version, there's a part of the game where the characters discuss the story of Urashima Taro. Since most Westerners don't know this story, the English version has them talking about Rip Van Winkle instead, which is not only very well known, but is pretty much the same story as Urashima Taro.
Also, when choosing what character to play as in the Japanese version, the choice to decide was "Ore wa..." and "Boku wa..." (Takeshi uses "Ore", while the Kid uses "Boku"). This wouldn't have worked in English, obviously, so the translators instead replaced the choices with the two character's respective situations: "I've got to find my friends" (Takeshi) and "Who am I?" (Kid).
The Cultural Translation isn't entirely perfect as You describes Rip Van Winkle drinking a liquid that advances his aging, which was an artifact of the Urashima Taro story. Rip van Winkle drank a liquor that put him to sleep for several decades. It also loses the Lemurian connection as Urashima Taro involved a castle under the ocean.