I was all but certain that it was Dr. Manhattan until that last episode where I began to think that it may be Lady Trieu, or possibly some combination of both or the two of them working in tandem. First, they establish that she can create humans (the couple she gave a son in exchange for their house & land), then Veidt tells his clone assistants that while he is their master, he did not create them. I don't think it's a coincidence that these two pieces of information were doled out in the same episode (unless they're intentionally trying to throw us off). But I also found it very intriguing that Dr. Manhattan was shown building a castle on Mars fairly similar to the castle where Veidt is held captive AND the thing Angela's adopted son, Topher, was building with the "Manhattan Blocks." Then both Topher and Dr. Manhattan destroy the structure they've built. I see a lot of parallels, but I don't quite know what they mean yet...