You seem to be under the misconception that I'm thinking of remaking Clue in its entirety in RPG Maker - I don't. I'm thinking of the *concept* of randomly generated murder mysteries, not using the mechanics of the board game. Remember, RPG Maker is not suited for multiple players, so there'd be no cards to distribute between anyone.
If I were going to make a game with, say, a randomly generated murder mystery, here is what I'd do, in concept:
* Break each plot into a number of pieces, say the Introduction, Key Event 1 through Key Event N, and a Conclusion.
* Start at the Introduction and pick a random one
* For each step, I'd have to know what permutations are allowed for the next step. For example, I probably wouldn't allow a combination of Key Events that made a single character be in two places at once, or required a character to be two other contradictory things at once.
* For each step, pick one of the allowed permutations.
* Repeat until we reach the Conclusion
The really tricky part is breaking each Key Event down into a set of NPC events and texts, and making sure that each set of Key Events which you allow form a coherent narrative for the game. By coherent, I mean where a player can, by experiencing the Key Events, see the Conclusion as a logical outcome, even it is a plot twist.