I think it's generally agreed that the sympathiser is a sucky role to be lumbered with. Not only that, but it seems to me that the negative abilities of both Boomer and Balter are backwards when it comes to how the sympathiser mechanic works - Balter has more chance of being a Cylon and Boomer more chance of being a sympathiser!
So I was thinking of this as an alternate way of using the sympathiser (still for 4 and 6 player games only):
In the initial loyalty deck setup, replace one Cylon card with the sympathiser (this means that in a 4-player game, there will *only* be the sympathiser card in the deck - no Cylon cards). After the initial cards have been dealt out, place the Cylon card back into the deck.
The sympathiser remains hidden for the course of the game, just like a Cylon.
During the Sleeper Agent phase, check to see if any resources are in the red. If so, then the sympathiser reveals and is sent to the brig. However, the sympathiser is now fully on the humans' side and will share their victory or defeat.
If all dials are in the blue, then the sympathiser remains hidden and will share in the victory or defeat of the Cylon side.
The sympathiser may reveal as an action, just like a Cylon. If so, they are moved to the Resurrection Ship, just like a Cylon, and are treated as a Cylon-allied sympathiser as in the normal game (i.e, no Super Crisis and may not activate the Cylon Fleet location).
In this way, Baltar is now more likely to be a sympathiser, Boomer more likely a Cylon, and the sympathiser has to sit through the whole of the first half of the game thinking about which side he should support more!
I'm also thinking that in a 6-player game, the first player to receive a Cylon card during the Sleeper Agent phase must *immediately* reveal (in the same way the sympathiser does in the normal game) in order to more closely mimic what happened in the show (Boomer "awoke" as a Cylon and immediately shot... well, you know who).