It's coming out in two parts, because it's got a lot more eps than the first season. The first part is out now. The second part should be out next month.
As for Season 3, I think there aren't too many to fit in one set. Isn't it something around 30 episodes? Simpsons seasons are coming out with 26 episodes per season (as far as I recall), so that would only be 4 more episodes than that, and it's not like they have buttloads of extras that they've been trying to fit on the sets :rolleyes: