Exploding skeletons, murdered people, a murder plot intrigue, good vs evil battle. This stuff just doesn't lend itself to random "funny" or if you go that way, you have to go that way ALL the way.
You pretty much summed up the plot of 98% of RPG's. And the content of 100% of RPG (although exploding skeletons might not be there in a non-fantasy setting).
And no, I don't agree the base premises of RPG-gameplay or story automatically means that the game also needs to be grim. Just as much that you can make a hack&slash game featuring GENOCIDE all dark and moody (Diablos I & II) or just really light and happy (say, Torchlight, and probably many more).
