To me it seems that Boomer as an unrevealed cylon is too powerful even when in the brig. Even when you know 100% she is one she just has so many ways to hurt the humans. While in the brig she can still:
Recon the crisis deck and dump the easy ones.
Play Evasive Manuevers and Strategic Planning to help the Cylon ships when they attack.
Try to escape each round while playing Scientific Research to make the humans burn cards.
She draws red and blue cards which help her mess with most skill checks.
Boomer can still be very devestating to the humans even in the brig and there really isn't anything the humans can do about it. I was thinking about making a house rule that she can't use her recon ability while locked up. She would still be strong enough to screw with the humans by virtue of the cards she draws and it would keep with reality. How the heck can she recon from a cell anyway?
What do you all think?

