

Buddy, if you think Naota and Mamimi’s relationship is in any way something to aspire to, or romantic, you have some growing up to do. I mean that as softly as possible.
She doesn’t actually have any feelings for him, she’s just using him to satisfy her dependency issues and frustration from his brother running off without her.
And as soon as he starts growing up and becoming more than a blank slate she can use for those purposes, she gets incredibly distant from him.
Anime in general isn’t particularly good for developing ideas of how relationships and romantic relationships should work, but FLCL is an especially bad one for that unless you really grasp the themes.
Nearly every character is just using Naota for something.
The class rep is the only one who really comes close to caring about Naota by the end, and it implies they may grow a real relationship, but even she starts out by using him.


Looks like no official explanation, but the leading theories are relating to the main character’s three main weapons or the three major figures of the story (can’t be more specific than that without spoilers).
I definitely never picked up on a specific meaning myself though.