A hub based power meter will give you the combined effort for both individuals.
I don't see any reason why the Captain and the Stoker couldn't have their own power meters... And they may not need to integrate the information at all. And, the stoker could simply keep his or her own meter, or give it to the Captain.
Since Garmin already does a single pedal... and interpolates dual pedal cycling.
You could do some thing similar, take a two pedal setup, and give the right pedal to the Captain and the left pedal to the Stoker. Then simply double the combined power. Hopefully your software could deal with the right/left differences.
One problem, however, with splitting the pair is range.
When I was reading about the Look pedals, I think one was setup as a master, and one as a slave, so the two pedals would communicate between each other, then send the combined info to the recording device. That may or may not work with 3 or 4 feet of separation.
Are you buying this through your LBS? Will they let you "demo" the system?