A scam perpetrated upon whom? On the viewers? Not if you've watched the whole series. All the clues are there, just mixed in with some very clever red herrings (such as planting the Ganger two-parter early in the season, with a duplicate Doctor in it, to get everyone wondering if it was the "Flesh" Doctor we saw on the beach...)

It's certainly a scam perpetrated on the Silence/Kovarian, though, and quite right too! =:o}