Most GMs wanna run a mystery game, at least once. Some of them, at least from those that I came to know, wanna GM a mystery campaign and not just a little game session. There is one problem that prevents them, "how can I come up with a new complex plot for each mystery?". For that, there is a simple answer: "You don't.
The longer version is more down to earth: After you've ran a complex mystery story, the players won't expect an easy and shallow one. More than that, they'll look for the rest of it. "No, it's just another red herring". After you've made a complex plot, with many stages and many more red herrings, coming with a simple one, a murder mystery at the level of an Action movie's mystery, they won't believe it's that simple and they'll create the complex stages for you.
Take into account, though, that after a very easy one, running another easy one will destroy what you built. It's preferred, at least from my experience, to go for one complex, one shallow, but don't make it too obvious. Sometimes, change of complex levels might be the refreshment the game needs.
On a side note, this can be used in conspiracy games also. When the players and their characters start to unravel the conspiracy, they'll look for more than what is on the surface. Doing all the work of the conspiracy in question seen to all will make them seem much more sinister...