Well, from my awesome o-o knowledge, there is season 2 for MANGA but for anime, least likely. It may come if a load of people request it but some people said it might come in 2014. Its just a rumor though.
posted over a year ago
Also, I checked the official blog- They had nothing to say about the second season, unfortunitly. Yes, I can read Japanese.
There's obviously going to be one. Ayanami said 'This is just the beginning'. And with what Frau and Teito were talking about, there's no way they'd leave it at that.