What makes an individual metaphor a good illustration of a complex idea as opposed to a "bad" metaphor that doesn't do the job of painting a picture with alternate words?
Well, first off, it should be a metaphor, not a simile. :) Ahem...
A great metaphor recasts the familiar or mundane as something strikingly different yet truly parallel. It gives a startlingly vivid picture or brings a surprising insight. A bad metaphor fails to achieve the parallel, or the fresh insight, or both. The element of surprise is an important part of a great metaphor. If we saw it coming from a paragraph away, it is far less effective; a metaphor can be bad merely because it is a cliche.
Some personal favorites:
"The wind was a torrent of darkness among the gusty trees/The moon was a ghostly galleon, tossed upon cloudy seas" (Noyes)
"The yellow fog that rubs its back upon the window-panes" (T.S. Eliot)
"Life's but a walking shadow, a poor player/That struts and frets his hour upon the stage" (Shakespeare)
"Out of the mocking bird's throat, the musical shuttle/Out of the Ninth-month midnight" (Whitman)
A good metaphor will parallel or easily invoke the idea you're trying to convey, without extraneous or irrelevant details. It resonates with the audience and may add to the core idea.
A poor metaphor has baggage of its own, doesn't track with the original concept, is too clunky, too esoteric, needs too much explanation, or becomes absurd.
A bad metaphor is like your 81-year-old Portuguese grandfather. Really, only close family members and people from that region can even understand him at all, and even then he's talking nonsense half the time, and he talks for far too long about things most people are unfamiliar with.
A good metaphor is a lot like a mime - it neatly conveys the essence of the idea in mind and requires no additional explanation.
A really good metaphor is much like Marcel Marceau - original, memorable, and even alliterative.