Well i played my game- actually it was by myself so it was more of a playtest than a game.
the game worked really well and the Cylon leader only just won. the cylon leader picked at random was number six and the agenda was the one where the cylons have to win but Galactica can't have more than two damage - Salvage their equipment.
I used all the skill cards, and crisis/super crisis cards, and characters from the base set and pegasus expansion, and used the Caprica objective with the Pegasus board
the game still felt balanced even though some of the game-experience was dumbed down. there was no loyalty guessing but that was intentional as i'd covered that with the Cylon leader option. a two player game is never going to feel the same as a 3-7 player game. However the random cylon agenda cards do create a 'what the frak is the cylon up to' kind of paranoia.
my character was even executed by failing a crisis card, and being human i lossed the moral too.
any crisis card that was pointless or unworkable was a 'no-effect', so for example where the president would have to give the title to the admiral became a 'no-effect' as the one human player already held both titles.
I didn't need to double up the skill cards the ratio worked very well and some crisis cards i just had to pick and choose to succeed on or let fail due to my skill set. but plent of the other crisis cards came up where a choice was to be made or the cylons arrived. so again i found the crisis card deck to be balanced enough for 2 player or even solo games
I allowed executive decision to be played on myself, but you could easily have one or two nonplaying characters chosen at random from the character types you didn't pick and only activate them with an executive decision card.
I reckon you could play a two player game with no cylon leaders by constructing the loyalty deck as shown in the exodus expansion, that way no one might be a cylon player at all, that would create enough suspicion and facilitate the need to hide your loyalty from the other player
anyway i'm going to give it another go with an actual other player so i'll check back in here again.