I just finished reading the last part, and I thought I'd tell you what I think.
First, the negative parts:
Sometimes it was fairly hard to follow. I couldn't really grasp some events---especially in the first few chapters---and I have to say at one point I was surprised to see that there was another Reimu with Marisa in the nest. I probably just missed the part where she was introduced, but it's still something that happened.
The fact that the little ones actually called themselves with "ko", etc. was kind of off-putting. I'm used to yukkuri calling themselves with their normal name, slurred at best.
I also didn't like the epilogue in its entirety.
On the other hand, when I could follow the events it was well written and the atmosphere was conveyed properly.