I think Moffat, like RTD, has a tendency to not let plot logic get in the way of telling a good story, and neither man seems keen on giving us what we expect (neither of these things is inherently a bad thing, but the downside is on occasion they can be).
I think the problem is this whole arc seems to be screaming "look how clever this arc is, look how clever this arc is!" in a way that RTD's stuff didn't - and if you want to play that game with the viewer then the arc story you are telling has to make sense - and so far this doesn't seem to or at least it provides no clues that the viewers can use to work out what's actually going on. If you are going to set up mysteries for the viewer, I always think they should have at least a chance of working out what's going on from the clues on the screen, we don't have that. Moreover, we just seem to adding question after question but no answers - even if we don't get all of the answers, the viewer needs some sort of regular pay-off to keep them engaged.