I think there is a conversion document somewhere on the AEG site for the old books to 2.0 (in the BBS).
Anyway, to the original question, I'm not sure what AEG has planned for Spycraft 2.0. Their website is pretty barren. You have to dig around their message board. (I probably should joing their mailing list, but I can't remember if I was thrown off of it or not. )