Substance:
I like to think that ending, where Yukari repeats her gesture with the robot from Chapter 17, implies that all they've shared, and Gaku's infinity-spanning heroics, remain in some way, and Yukari stays because a woman who'd go to such lengths is worth so much more than personal advancement.
I agree and think that is what happened.
This was a trip. Found it at midnight last night and read it in one go.. Good thing I didn't work today. I can't express enough how much I love it, and the comparisons to Lain are pretty accurate.
Trippy stories like Evangelion or FLCL aren't quite as interesting to me as they used to be (though I still love them), but the ones that manage to maintain a coherent story despite all the weirdness, like Qualia or Lain, are still some of my favorite types of stories to read. Probably this particular mix of sci-fi is one of my favorites too, reminding me of Gibson's books for one.
And I can really understand Gaku-chan, myself. Like her, I can feel the desire to go that far for someone, if only I had the ability. And even in the end, though I share her mild frustration with not finding a "perfect" solution, I can also understand why such a thing is necessary. I'd be too selfish to remain a non-existence, for sure. I'll end up rereading it, probably in the near future, but frankly I expect this to become one of my all-time favorite mangas.