I dunno, I think they should focus on making SG Atlantis the best it can be. First season was slow, second season got better somewhat (haven't seen 3rd yet).
I thought SG-1 was weak, that Atlantis was the better of the two. If they make Atlantis a little edgier ala Babylon 5 or BSG it could rock.
My ideas:
Atlantis: Now that Carter is there, kill off Weaver and let Carter take over.
New Series: SGC decodes use of the 9th chevron, teams start exploring other time/dimentions or alternate realities.