If you've been watching CM this season, you know about the person who's been copy-catting a lot of the BAU's cases from this season.
They have also been stalking the team, getting freaky close and even torturing them (Zugzwang ring a bell?). They've been very good at keeping the Replicator's identity a secret though - but I have a theory who it is.
We saw him leave the show a broken man. In my experience, a man can never truly turn away from all that he's accomplished. What if Gideon's burnout eventually became a break, and he holds the team responsible? He has the knowledge of (most) of the team to pull this off, and the intelligence. Plus the fact that we've seen the Replicator using old school chemically developed photographs.
As I said, this is purely a theory, but I'm interested in hearing what people might think.