omg. also, goddammit, Joss.
OK, so first of all, I don't believe Whiskey necessarily came back as a sleeper. Or rather, I don't believe that her killing of Bennett was a sleeper action
I believe Claire Saunders killed Bennett herself, specifically waiting until Topher was in the room so he would have to see it and get blood splattered all over him. The look she gave him when the deed was done seemed to indicate that she kind of wanted to say "Happy now?" The sleepers haven't tended to speechify before carrying out their murderous orders like she did, which makes me think that was her own choice.
I get the idea of bringing Mellie back because she trusts Paul, but ... why not just imprint November/Madeline as a badass ninja instead? Mellie is actually fairly helpless and extremely useless. Unless you're hungry for lasagna, then she's your girl.
I'm also going to go way out on a limb here and say that I don't think Boyd is really the head of Rossum. I think he's in a similar position to the one Paul was in, but he's smarter and better at his job. So much better, in fact, he was able to infiltrate the Rossum offices, kill the actual head, and stand in for him/her when Caroline came to visit, then put himself in a position to be her handler later on.
Either that, or he's an active (we've never seen him near a disruptor!) and was imprinted as the 'head of Rossum' when he met Caroline, and has since been imprinted more or less permanently to work in the L.A. Dollhouse.
Otherwise, I just don't get his motives. Why would he engineer this situation? If Caroline was such a threat, why not just kill her? Why is he allowing all the other insurgents to live, knowing exactly what they're up to?
Unless it's just a typical case of the big bad creating his worst enemy. Caroline isn't some mystical 'Chosen One' like Buffy was, she was chosen by Boyd, which only then made her special. I really hope one of my other theories is right, because I really don't want Boyd to be the Big Bad.
I think this show could have succeeded if the episodes had been sequenced a little differently (and obviously altered slightly to account for continuity issues introduced by changing the order). There are two possibilities:
S1: Man on the Street, The Target, Grey Hour, Needs, A Spy in the House of Love, Briar Rose, Omega, Vows, The Public Eye, The Left Hand, Meet Jane Doe, A Love Supreme, and an episode wrapping up the Alpha arc and firmly establishing that Echo is becoming a real person.
S2: Continue Echo's growth arc starting at the beginning of the season, working towards Stop Loss/The Attic in the middle, and allowing for more space to tell the whole story (the last few episodes have seemed rushed to me) that will be wrapping up next week.
OR
Start with Epitaph One and work backwards from there. There are enough gaps in that episode that it would take a LOT of show to answer the question of how they got from point A to point B.
Either way, we're headed for one hell of a finale, which I'm taking to be next week's episode. Epitaph Two should serve more as a coda, since it takes place well after the current timeline. The story that started in The Public Eye, though, has to end next Friday.
I hope the next thing Joss does is fully independent and doesn't suffer from network meddling.