What’s an anime detail most people miss, but completely changes how you see the story?

The flowers in Anohana aren't random - they match the grief stages perfectly.

Thats called forehadowing and yes AOT is an anime that really excels at it.

This isnt something I noticed later or anything, but for Orb for instance the way the setting gets introduced and later again can be easily missed by people but will very much effect how you interpret a lot of the anime

A lot of anime I watched when I was a teenager had messages that I wasn't able to catch until I rewatched as an adult.

Kiki's Delivery Service was just a "daily slice of life of a witch" to me when I first watched it, but upon a rewatch more than a decade later, it's a very good portrayal of the anxieties people experience when undergoing life changes and challenges.

Isayama is a genius. You can keep going back through the manga and anime of AOT and still find new things

**Shoshimin**. Seemingly random tiny details and throwaway lines such as the repeated display of the current time turned out to be relevant down the road. That’s just one of the examples – the show is chock full of them.

That's what I liked about Naruto:

1. How Naruto "cheated" the written exam.
2. How/why Kisame recognized Tobi's real identity.
3. The true identity of all six paths of pain.
4. Tons of fights relied on deceiving your enemy, thanks to being able to transform, and create clones and illusions (I'm keeping it vague or else my post will be banned for spoilers).
5. Figuring out Hidan's ability.
6. Figuring out each Pain's ability and limitations.
7. How Sasuke tricked Danzo.
8. The truth behind the Uchiha Masacre.

Many of those things were there if you were paying attention, and it's stuff you can figure on your own or at least strongly suspect before they get shown or explained.

It's a real shame the last arc lasted so long and devolved into "my kamehameha ball is more powerful than yours" and "I'm the final villain behind the final villain, behind the final villain, behind the final villain all long", because up until that arc, the series put some thought on leaving breadcrumbs and reasonable explanations compatible with established lore.

I don't seem to remember anyone talked about how Mikasa's reaction after she learned Eren's death in EP7, which is one of the most psychological accurate depiction of such reactions I've ever seen

In FLCL, when you realize what Haruko is. At first she seems like a quirky hot chick, but on second viewing how much of a villain she relly is and what she symbolizes. She is a warning to teens about older people that might seem cool but are actually seeking to exploit them. She is a warning of child predators and creeps that go after teen kids.

Also Grave of the Fireflies. at first viewing you think is a tragedy of kids dying becasue of the tragedy of war and shitty relatives. but in fact there is a message similar to the cricket that froze on winter. The big brother spent all time just playing and stealing and not working to survive. that is why he and her sister died.

In Madoka Rebellion you have short messages displayed in these witch runes. Most are neat little references and quotes to the themes and inspiration of the story (especially Nietzsche and Goethe's Faust). But one really stood out for me: "They glorify death."

It really hammers home Homura's motivation and despair that ultimately lead her to the decision she took at the end of the movie and why I see Rebellion as a perfectly logical continuation for Homura as a character. It's a condemnation of both the other magical girls and the viewers that are content with the situation at the end of the main series.

In *Your Name*, the plot of the entire movie is shown in the opening cutscene of the movie as the credits roll. 

The amount of current Pokémon watchers who don't watch other anime and don't understand that the development is through how Liko Roy and Dot battle and not the result of the battle is disappointing. It even spells it out in episode 56 of Horizons and it's a detail that is being forgotten about.

A *lot* of Evangelion is reframed when you know what's actually going on. Episode 9 does a great job at reframing the viewer's opinion especially if they know what the Walls of Jericho are, and Episodes 21 and 22 bring it all into perspective ahead of the finale. Eva is a show designed to be rewatched.

The finale of I Parry Everything was a fantastic episode which explicitly alleviates the concerns the viewer may have about Noor. It frames his powers in a way that makes some of the earlier moments make more sense. Parry can be enjoyed on multiple levels but it does give you a lot to think about instead of Noor just being an idiot, when you start to ask why he thinks like that the finale does a great job of confirming it.

I feel like the fact that all of Evangelion happens in a post apocalyptic setting where a lot of the world is no longer habitable is a detail usually lost on people discussing the character decisions. They can’t go somewhere else, they can’t do much else. They’re less depressed and dysfunctional than a lot of modern people and they have it way worse.

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In Spy x Family, Anya lies about her age to be adopted, she's a year younger than her classmates, which is why she's a bit dim-witted

In One Punch Man, I like a little-explored aspect (which could be really profound if the theme weren't comedy) which is the main character's motivation. He fights because he's bored, sure, but if you analyze it, he describes this boredom more deeply, describing it as a feeling of emptiness.
What he's looking for is more than an opponent, it's a thrill, a goal, what he's looking for is a purpose.
or something like that :p

Both Shio and Satou are severely broken in Happy Sugar Life to the point the only societal depiction of love they know is the imagery of a wedding. They are obsessed with the pureness, and don't understand love can be familial.

In reality, they are really more like mother and daughter 99% of the time. It means the story is NOT a yuri.