Join Date: Jul 2006
Location: Buenos Aires, Argentina
Bikes: Co-Motion Mocha, Trek T100, Schwinn Fastback Comp, Specialized Stumpjumper
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All things being equal, you'd want the heavier rider as captain, but cycling skills can easily compensate as long as the stoker does not throw his/her weight around (which would be a problem in any case even with a light stoker).
So the answer really is what works for you, if you have the luxury to test it. Many of us don't have the option of switching with the stoker because the shorter rider often is too small for the captain's bike size.