I found out the answer. I heard an interview with the producer recently and he said as follows.
The original plan was to have Micheal Palin as the host, and two teams - a "clever" team and a "dim" team.
Alan Davies was going to be team captain of the "dim" team and Stephen Fry team captain of the "clever" team.
But Palin did not want to do it.
When time came to film the pilot they put Stephen Fry in the hosts chair till they found a "proper" host.
He was so good he kept the job, and they just never bothered to get a team captain for the other team.
http://www.qi.com/