Yep. And most good writers wouldn't have made it so blindingly obvious. Lost in Space did the "guy sabotages the ship" thing, but a) it was 1964, and b) the doctor was the obvious villian through the whole thing. It wasn't a mystery, and nobody pretended it was.
Gilligan was funny, but I can't imagine how stupid the whole thing would look if GI went the same direction as Lost.
Now that you mention it, most of the other mysteries are definately the X-Files style shadow government conspiracies. Dharma is a shadow government doing psi experiments, and the Hanso Foundation is another shadow government making ultra weapons.
Somebody call mulder and scully.