Clue is exactly nothing but a 'process of elimination' game, but it has no clues in it. That is the 'clues' are simply 3 variables which can each take on one of several values (location, weapon, perpetrator). Each player simply guesses different combinations until they have eliminated all but the correct answer. There is a modicum of skill which consists of noting the various guesses. Careful tracking of eliminations can get you to the answer in the least amount of time, but there is one fairly obvious optimum strategy. Most germane to the current discussion there is no 'fiction' involved (at least which matters). Nobody is questioned, no clues are actually gathered, and nothing either mechanically or fictionally justifies one's guesses, nor explains fictionally the mechanism of eliminating the different solutions, cards are simply revealed to do that. The point being, it isn't possible (except by bad record keeping) to be mislead or 'miss a clue', etc. So the game has nothing to teach us about RPG mysteries.
I guess you could say that, to the degree that Clue serves to provide the feel of a mystery, then you could model an RPG mystery process on it. This may suffice for whomever is not particularly interested in really 'playing detective' and simply wants to run around to different locations making vaguely 'crime solution-like statements' and having the fun of eventually being right. Dressed up well, this may in fact be quite sufficient in many cases, and is probably better than a more straightforward process which ends with the players totally stumped and unable to move forward.
So, I kind of agree with you, Clue does provide a model. Just don't be fooled into thinking it is a model of actually solving a mystery!