The art went through many transformations, partially due to experimentality, and then also taking advantage of multiple styles to be expressive at different points. I rather like the effect (although I rather liked the more deformed early Dr. Aoi. He was pretty cute that way

)
The ending was pretty awesome to me, because it really jumped up and did something I really cynically didn't expect. Not that I'd have been disappointed if it worked out anything like the direction I guessed it was going, but it was like,
wow! That's awesome! I really, really liked it.
To delve into spoiler territory for those who haven't read, I also really, really liked the fact that the story commitally dove into actually assuring us that the main characters (to what extent one's left to wonder, really- who's to say they didn't actually go back and save
every last person? I mean, Heliotrope
was a superhero, right?) got to live such an open-ended, wondrous, probably eternal sort of life, exploring and learning... that's just damn cool. It's like having a story tell you that it's characters all went to heaven, but instead of being pure magical fantasy, PDH came up with a reasonably scientific idea for how and why it all worked out, and it was such a simple thing to pull off in the end. That's just.... really awesome.
And "puppet" Aoi was pretty darn cute too.
