I've been going back through the old forum threads and it seems that the Sympathizer Card was not so disliked in the early days. However, as the game got played more and more there seemed to develop a general consensus weak component. FF did give a no-sympathizer variant, along with other variants, on 12/18/08.

So am I right, do you still loathe the sympathizer card and if you do do you use the FF "endorsed" variant?

We haven't tried it, and it's hard to see how it would turn out. It might be worth a try, but there is a more fundamental problem with a 4 player game; a cylon player faces three humans in terms of actions done, or opportunities to make good while humans are recovering. Alternatively, if you are playing with the sympathizer, it's 2v2. I find that each of these are at extremes in terms of actions.

All the same, it might be worth a try!

We routinely use it in six-player games in which no one chooses a Cylon Leader character. The variant works just fine, since there is still a cylon team (rather than a lone cylon), and there's no need for the unthematic metagaming that bothers some people or, more importantly, the unfun of ending up a sympathizer. If anything, it makes the game a bit more interesting for the cylon players, since they have more chance to affect crises after they reveal, due to drawing a third card on their turns.

We tried the variant once with a four-player group, and the one cylon player said he felt like the odds were really stacked against him. We don't play four-player BSG any more, so no more data than that.

We just use the Sympathetic Cylon option from Pegasus; we always hated the Sympathizer card and before Pegasus we would try to play a 5 player game so it wasn't an issue. I can understand the concerns some people have about drawing an Agenda mid-game and how difficult it can be to win, but personally I love it. The last time I drew the Sympathetic Cylon card mid-game I had players on both teams convinced that I had virtually every "Humans Win and..." and virtually every "Cylons Win and..." card that is found in either Agenda deck! My Cylon buddy was convinced I was a traitor for 90% of the post-sleeper phase and even when the game was over and I announced that I had won the other players still didn't know what my Agenda (Salvage Their Equipment) was!
I really like the mid-game Agenda, it makes you work really hard sometimes, unlike playing a Cylon Leader who draws "Humans Win and you have played a SC card" which is a pathetically easy goal if you start the game with it.

I have always played with the official No Sympathizer variant. All my groups prefer it. Like the official rules say, if there is a seeming imbalance then adjust some resources downwards. The Sympathizer irritates us, better to toss it and fiddle a bit with the resources. We keep the rules for resources as they are in the official variant, and have no regrets