A traditional drivetrain has three spiders. Both left-side spiders would read captain power, and the right-side spider would read total power. It'd take a head unit that could take two power meters as input and do the math to derive the stoker power.
You're right about the pedal-based power meters, IF they make it to market as suggested. I'm also curious to see how accurate they are - there will be two new layers of imprecision with them. Crank length will have to be entered into the head unit, and that'll complicate the head unit's math (probably handled by a firmware update). Also, the strain gauges won't all be aligned with the direction of deflection like hub/crank systems, so they'll have to combine readings "between" gauges.