So we played our first game with Pegasus yesterday. We had 5 players, and one selected Cavil, so got one of the "hostile" 5 player agendas.
It might be that we were missing a rule, but an infiltrated Cavil seems immensely powerful. While infiltrated, he can still Primacy up a whole bunch of Cylons and walk around brigging/executing people. And he can still Primacy from the brig. There didn't seem to be any reason for him to ever STOP infiltrating, and in the worst case scenario he just sits on the Resurrection Ship until his next turn (and you've wasted a human action executing him, and likely two human actions brigging him first then executing him.)
The agenda seems to make it so that the Cylon Leader player is playing an entirely different game than the other four players, which just happens to be played using the same gameboard, and there seems to be very little you can do about it as one of the other four players.
So we're thinking we were missing something obvious that slows the Cylon Leaders down?