The first action is to pick a unique and unusual location. For a strange and unique mystery. This goes back to keeping things simple. Allow the wonder and confusion to stem from one part or the other of your story. Too much can create chaos in your reader.
Limit yourself to five or fewer suspects. Not only does this make your story more tight and concise, but it also makes it easier for your reader to keep track of the clues and hints.
Create subtle connections to each character to create cohesion. Your supporting characters are suspects by design. Each one should connect to each other in subtle ways. This will tie your story together in ways that will leave your reader reeling, but in a genuine way.
Eventually, it all stems down to; The intensity of your mystery will arise either from the characters or the intricacy of the crime. It is best to stick to one or the other, and you should have success.