To indulge in a lame answer, why not? (This may contain spoilers since there's also my own odd analysis. You need to highlight the whole big blacked out section in order to see it. (Note that what I know about RahXephon is through the series and movie, not the manga).
Itsuki is one of my favourite characters of all time. Complexity and growth throughout the series you'll follow this change as you get to know him more. This is not present in the movie, RahXephon: Pluritas Concertio. Throughout the series he's pining away as he grapples with rejection and being second best even though he's obviously this highly intellectual individual that is revered in addition to being the best doctor (scientist) in TERRA. As the story unfolds so does each of the characters and he's no exception.
There are several triangles within the series and he is part of two very obvious ones, both not only deal with love but his very place in the world. Itsuki displays a desire for Haruka throughout most of the series however she is very much still in love with Ayato. If you’ve read the summary, which contains spoilers, or you’ve seen the series, then you know how much that has got to be an odd situation.
Itsuki is Ayato’s younger brother, so not only is there the question of wanting to be with another person that rejects him, but also that he ought not even be in existence and that he’s a “filler” for his brother. Itsuki’s existence is annihilated (that was horrible) when the world was changed to the way it “should have been.” I’m sure that prior to that Itsuki was aware of what would happen when and if the world was “tuned.” Even he wanted it for Haruka, which means that he would have sacrificed himself for her happiness. To further complicate the issue, Nanamori is madly in love with him and he’s seemingly oblivious.
There’s the question of love though. Clearly throughout the series he is protective of Quon. Even though he displays a desire for Haruka, he is highly protective of Quon and then (from my understanding) it turns out that she’s the one he’s been in love with. Upon his death, he called his dying image of Quon the bluebird – which was actually Nanamori, who just stabbed him.
The other triangle which lacks the sting of love is between himself and his two childhood friends: Helena and Makoto. The story of the Wizard of Oz comes up here; actually they use a few analogies. Itsuki is the “cold” one, cold as champagne, something attributed by Makoto. Makoto doesn’t ever quite get an analogy if I recall correctly and Helena is more of the heartless one. As children however, Makoto is still full of hope and spirit but hateful of his label as a “D.” In fact, between the three, raised at the Bähbem Foundation, Helena was the best, the most likely of the three to become an instrumentalist. Itsuki, scared, but willing to go along with them all while be close to Makoto was the second. Itsuki seemed to serve as a purveyor between the two as Helena and Makoto seemed to be extremities. Back to the Wizard of Oz, that which was pictured was specifically the Cowardly Lion, the Tin Man and the Scarecrow along with Dorothy stating what they each wanted. I attributed the Tin Man, that which was in need of a heart, to Helena. The Scarecrow to Makoto, though often I feel like the two are interchangeable. The Cowardly Lion to Itsuki, for he seemed to have needed that.
Back to the topic at hand, I adore Itsuki for the way he changed throughout the series. It all seemed plausible. Plus, it didn’t hurt that he reminded me of one of crushes.