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RahXephon (in response to ANN's podcast).

He claimed that at the end of the day, all the show had to say was that "love is awesome and people deserve to decide their fates". On a very, very basic surface level those are indeed among its core themes, but that's a terrible oversimplification.

On one side, we see the Mu, who know that the world's tuning is imminent. Their blue blood marks them as the elite, and they wish to control what the new world will become. The humans, of course, don't like having their fates decided for them even if the Mu aren't exactly ill-meaning (they're not benevolent either, mind, they have goals and they're willing to shed blood of both colors to achieve it). However, the Mu themselves have overreached their boundaries and aren't as in control as they may think they are, this becomes particularly clear through Maya. Actively seeking to control the fates of others isn't within man's jurisdiction, in their attempt to control the fate of mankind the Mu themselves were manipulated by Bahbem, who got his own just desserts in the end.

Ayato doesn't have any particular interest in tuning the world, he just wants to live his own life. But as he quickly discovers, you can't find happiness through apathy toward the world around you either. That's just running away, it's self-destructive and it hurts the people who care about him as well. What always strikes me about RahXephon was just how personal (and interpersonal) it is. The world he ultimately creates wasn't born out of some grand vision for the future of humanity, but out of a simple desire for a place where he can live out his life with the people he loves. In that respect, he manages to find the middle ground of taking the initiative to control his fate without forsaking nor abandoning the people around him, simply focusing on building give-and-take relationships with the people around him. The world that results isn't perfect, but it's one where he's found happiness by doing what he needed to be doing all along.

"winning the girl by daring greatly and overcoming adversity"

A theme can't be summed up in a single word; "love" and "agency" are raw concepts, the theme is what the story decides to say about them

and the premise is the setup that the story uses to convey these themes

the characters' psychological states and visions for the new world, how they choose to confront their respective roles in a world that's nearing its end, what direction they wish to guide that world's future down, etc.

The Mu want to control Ayato's destiny for their own purposes, they're neither malicious nor benevolent but their intentions for the world's tuning clash with Ayato and with red-blooded humanity. Conflict. Terra doesn't wish for the world's tuning at all, they want to defend the world as they know it, which positions them against the Mu, but their best weapon against the Mu is the agent for their enemies' ambitions. Conflict. I could keep going. It's not about what the characters do, but why they do so.