They paired it with a OPG that doesn't really benefit a Cylon; actually its a pretty crappy OPG in general. Other than his skill set I don't think much of him and would take any other pilot every time, except for Anders of course.
Troublemaker - If no one else in addition to you contributes Skill Cards to a Skill Check, remove all Skill Cards that you used for this Skill Check.
This doesnt really seem useful; on his turn it does nothing and the group will be deciding whether to pass or auto-fail most Skill Checks anyway, so I don't see what you had in mind with this idea…?
Ellen Tigh is maybe the closest to having a weakness that hurts a team because she draws treachery, which is always beneficial to the cylon team and not the human team. However, this is still a drawback for the player of Ellen Tigh, even if it is an unrevealed cylon, because all the human players know to be looking at her whenever treachery comes up.
I gotta disagree here too, she should be discarding the Treachery to move around or throwing them away on Skill Checks you plan to fail; her ability to pass out XOs is so solid that the possibility of her spiking a Skill Check doesn't matter. Most Treachery have low SC value so she can't do a whole lot of damage as a Cylon, and its pretty obvious to the rest of the players when shes up to no good.
Boomer's "bad stuff" hurts a team a lot more; if shes Human after Sleeper then they have to waste cards and actions to get her out of the brig, and if shes Cylon then her reveal power gets shut down.