Count me in as another pissed about the lack of recognition for Tatiana Maslany. The person giving the best performance on television not being nominated for television's top award makes it impossible to take them seriously.
The window of eligibility for Emmy nominations is June 1 - May 31, so Season 1 is the only season eligible, since Season 2 premiered in June. I sure hope Lorraine Toussaint is recognized next year! Also, I believe Uzo Aduba wasn't a series regular in Season 1 which explains the Guest Actress nomination, though I would think she's most definitely the front runner.