This came up last night as someone wasn't happy they could not choose Boomer in the 6 player non-sympathizer variant:

Why are you not allowed to pick Boomer? Is there some sort of balance issue with her "Go to the Brig" drawback? Or is it because of component limitations for the extra "You are not a Cylon" cards? If that's the case, why not say, "Boomer and Baltar cannot both be chosen in a 6-player non-sympathizer" game?

Any ideas?

I am assuming it is a balance issue. Her negative is getting a 2nd chance at the Cylon cards and statistically having better odds of being the Sympathizer. If you take that role out of the game, it diminishes her negative and makes her a stronger character.

But it probably wouldn't upset things that much if you really wanted to keep her in and make some modifications. A lot of people are reporting back the character distribution during setup is not necessary for keeping a balanced game.