I can't accept Yukari and Ran abandoning Chen, it makes no sense with the characters and it's pointless with regard to the story. If Ran and Chen were both left behind it would work with the story where Yukari herself is vanishing, but having the two of them vanish and leave the third behind seems gratuitous at best.
The whole story kind of seems like that though, while it covers some events, it avoids getting into much depth about any of them. Yeah, you've got the emotional "everyone shows up to bolster the hero" but the story doesn't earn that with much lead-up, or in fact much of anything but a few minutes of Reimu feeling sorry for herself. Which is sad since there's so much potential to the concept. Was the gap youkai never really needed? Maybe something has changed and only now she's not needed? Maybe Reimu will take her place and become a youkai? I'd love to see stuff like that dealt with in a story, it's fascinating.
Unfortunately, this isn't that story.