I think the overall story was really well done. The actions people took didn't feel too crazy and I don't think there were any faults in the writing. The pacing was very very well done! I never found myself too bored or spaced out because one thing after another kept happening.
Sakaki's role in everything was... Odd, but fine. I think the "secret" was a bit too messily done, I mean, how would they know? Why would they do X thing when all of this was forced upon them?
But I think all of that is fine.... Except the ending. It really felt like they weren't really sure how to end it. They really didn't need to end it as such and really could have gone the "less is more" route.
Overall I think it's about a 6.8/10. Worth the read for sure, but it's probably not a series you'd write home about.