Shiki, Summertime Render Recommendations
Summertime Render has the same small village type atmosphere that Shiki has. Odd things keep happening, quite literally, in the shadows. People get replaced with a superior version of themselves and the main protags need to fight off the intruders.
It's similar in the aspect that the reader has the awesome foresight to know what's happening already while the actual characters gradually put the pieces together as the chapters continue on.