Concerning decoupling clues from locations, though, that only sometimes makes sense. It's commonplace for a piece of evidence to only be meaningful in a particular context, and sometimes that context is the location in which it's found.
That being said, if you can't move a clue, it becomes more important to make sure there are multiple ways to learn about it. Maybe if the PCs don't see the muddy footprint in the garden, the gardener did.
Nah, Mafia/Werewolf is actually a third option, and served by games that exist outside "our" roleplaying industry. Look into murder mystery party games for that.
By "mystery-shaped storytelling" I mean more stuff like Brindlewood Bay, InSpectres, Technoir... stuff where even who did it and how just isn't decided at the start.