I get the feeling that that frame of them all standing in the HQ that has Joe with his gun drawn is them facing Wells, and I bet money that Wells is just Wells this time around and there's going to be a bunch of "how can we be sure this isn't the guy that tried to kill all of us" going on for just a little too long this season.
@_nox_: My theory had been that Snyder was going to do one more Joker story in which he literally messes with Bruce's brain to bring the Batman back.
But, your theory seems more likely. Maybe current Bruce dies and Alfred uses the cloning machine out of grief. Or Jim retires as Batman because he fails to save current Bruce from something and Alfred uses the machine because Gotham always needs a Batman.