I was mucking about and came up with this for an Athena character, as a cylon leader:

Sharon “Athena” Agathon
Cylon Leader
Skill Set: 1 Piloting, 1 Tactics/Treachery

Earned Trust: On your turn, after taking your action and if you are infiltrating, you may draw two skill cards of different types.
Vision of the Opera House: Action – Once per game, you may look at the top six cards of the Crisis Deck. You may put any of them back on top of the deck in any order, and the rest on the bottom in any order.
Family Ties: Sharon “Athena” Agathon may not use an action to return to the Resurrection Ship while infiltrating.

Starting Position: Infiltrating in the Hangar Deck

My goal was to make a cylon leader character who played differently than the others and was better infiltrating than cylonning.

The only real problem I see with it, is the great difficulty for the character to make it back as a Cylon. It would in fact neuter the character by eliminating half of the game mechanics. Additionally, if you draw the wrong agenda card you might never win! (The one where you have to use a super crisis card) If the humans never execute her she can't play her super crisis. If you tweak the flaw a bit I think the character becomes more playable.

Yeah, I can see that being a challenge.

I wanted to make her want to stay infiltrating, but her drawback also makes a hard choice for the humans as to whether they actually want to execute her (of course, she could just airlock herself... and the humans might even try to stop it).

She probably would be better as with a Sympathic agenda.