We can't keep the clones forever, I think Cosima will be the first to bite the dust unless that cure thing is still in the works. There's also the issue of Rachel coming back since we can assume the pencil in the eye didn't really kill her. This was the statement released a few days ago in regards to the season three synopsis:
Season three plunges the clone sisterhood into unexpected territory with the realization that they’re not alone. Just when they thought they knew their enemies and allies, season three reveals our clones are more vulnerable than ever before. Highly trained, identical male-soldiers raise more questions than answers. Who are these new clones? Who created them? And more importantly, why do they exist? Sarah, Cosima, Alison and Helena are stronger together than they are apart, but this season will put that bond to the test. Will they forge towards their truth, or fall at the feet of those that seek to control them?
It doesn't give us much but we're clearly opening another can of worms, but I expect the crazy religious guys to still be around, same with Art and the like. Things are just mega complicated right now.