I can't comment on BSG, not seen the new series as I don't have Sky, so I'll have a better opinion on that when I get the first season on DVD in late March. I loved the miniseries though, and every review I've read of the series says it is just as good if not better, so really looking forward to seeing that for myself.
Atlantis though is just going from strength to strength, and the two part season finale is incredible, no idea how they pulled that off on a tv budget, talk about wringing every last penny out of the budget. Even the secondary characters are well rounded and well detailed, everyone gets a good share of screen time and lines (well except Lieutenant Ford, who seems to exist solely as Major Sheppards shadow). My favourite characters aren't even main cast, as they are Dr. Carson Beckett (who is frankly hilarious) and Dr. Radek Zelenka (also funny, and useful counterfoil to McKay). Quite what they are going to do in Season Two I have no idea, but with the Wraith they have a genuinely creepy threat to fight, and whoever thought up the Genii should get a pay raise!