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.
Accidental Aesop: The whole film can seen as a deconstruction of Fanservice and how a series should never rely on it to gain viewers. Because at the end of the day all you've done is objectify and humiliate a human being. Remember, this film was made during a time where anime Fanservice was absolutely tame compared to today's standards and before anime wasthrown into the ghetto.
Adaptation Displacement: A comparatively mild example; it's fairly frequently mentioned that it's based on a novel, including on the DVD case for the anime... but you'll be hard-pressed to find a Westerner who has heard of the novel outside that, or knows anything about it.
Hell Is That Noise: Several sounds/songs, like "Virtua Mima" which is mostly played during all of the high-tension/insanity filled scenes. The song makes use of the sounds of chimes, bells, and metal clinking together... the percussions almost resembling the sound of one's heartbeat. There are several whispery thin voices singing soulfully, not necessarily in chorus as the play of notes travel erratically from high to low (soprano to bass). It all comes together to resemble some rather creepy sounding tribal music. It's the kind of music that will make you want to dive under your bed covers and stay there for a while.
Uncanny Valley: Mima goes through a journey filled with all kinds of things nightmarish throughout the movie, and while most of the character designs lean toward realistic, there are two notable exceptions: Me-Mania, who is obviously creepy-looking from the start, and Rumi, who, like him, has eyes that are too widely spaced.