I'm sorry to not see or hear anything about this recently, I hope that isn't a bad omen.
To be honest, and this is difficult as I haven't seen the pilot (so take this criticism in that context), I dont get the show.
It does seem like a whole lot of preaching to the converted, and not just that but (maybe this is the wrong idiom) a bit of floggin' a dead 'orse.
I gather you are aiming for Myth Busters genre, but as a more specific attack on pseudo-science. Well the problem is, where's the mystery, where's the surprise in the show. In Myth Busters - as Adam Savage said on the SGU podcast - even the producers don't know where the show is going. But this almost seems like a glossy presentation of the Skeptoid podcasts.
Don't get me wrong, I'll listen to the skeptoid podcasts for the content, but if I want to know the outcome I just have to read the title. After two minutes of a skeptologists episode people will know - oh, this week they tell us that wheatgrass and ghosts are nonsense. It's a foregone conclusion that you will bust the myth. Despite it's title Myth Busters has the mystery of the outcome, will it be busted or confirmed? The producers and the audience don't know.
I've got to agree I don't like the title either. (although I like the microscope S in the logo)
I'm 50/50 on whether skeptic should even be in the title at all. Skeptics Guide to the Universe is better, as suggested, so nice one for going and using that right up. I feel bad for not offering another title but it's tough one.
You talk about how atheist is a dirty word, well I think skeptic is almost as bad. It's a turn off - synonymous with 'closed mindedness', that is to the people who you really want to reach.
You know what I thought was a really good title - Here Be Dragons. Maybe you could even recycle that.
Id have to agree with the equal representation of women, rather than a proportional representation. That way you might have a better chance of reaching more women (and if they are hot, more men), but specifically women, which I know is a goal of the skeptical movement.
As I said, I'm not sure of the exact format, so maybe some of this is redundant, but I think you need an element of surprise to the show. Maybe a format that is a reworking of Science or Fiction. (Maybe that's a better title) You could go with three or maybe with two subjects. There's always the issue that people could leave and forget which one was which though - but the point is really to promote critical thinking, not just conclusions.
I've got to say, the cast looked pretty big too, was it 9 of you? I know you split up, but I think that 4 would be more accessible, you can always bring experts in for certain segments.
I sort of like the idea of having laymen on the show, whether it's the public, some students, or a studio audience.
Maybe it could even be aimed at kids, and have some kind of game made out of it that ends it someone getting gunged. maybe that was just appealing to my generation when we were kids though.
To sum up - my main issue is the foregone conclusion of it. I'll try and think of some more constructive ideas to post that would solve that but it's a tough one.
All the best with the show.