Awesome series. I agree- the last episode was the best yet. Especially the "baptism" scene.
I'm almost certain that the man with the tree tattoos is Scutter. Though, now that I re-read your post, I don't see anything to indicate otherwise. Ah well. At any rate, whomever acquired the carnival seemed to do so specifically because they felt it helped their quest to find Scutter- if, indeed, he's even still around, and not just wandering around in dreams.
Since I've only seen each episode once, it's hard to go back and put things together. But remember in the first episode, where Samson was talking about the war between light and dark getting played out in every generation? My guess is that, in the last showdown (possibly during the Great War), something went wrong, and things weren't fully resolved. If that's the case, Management could be the opposite side ("good", for what that's worth- he was willing to sacrifice a girl to the ghosts in Babylon simply so Ben could have the experience in the mines) looking for Scutter to finish things off- meanwhile, events have moved on without them, and Ben and Justin will be getting caught up in both the past and present showdowns.
All this is speculation, mind you. I could be totally wrong. For a while I thought the snake lady (can't remember her name) might be Ben's real mother, but the last episode proved me wrong on that. At least, I really hope it did.
I like all the stuff with the templars and occult history. It's something I wasn't expecting; there's a lot of backstory to go through, but they're mixing it in with current events enough to keep both plot threads interesting.
Incidentally, I've been told that the second season has been approved, which is why there doesn't seem to be any resolution immediately on the horizon. I like the show enough that I'm not irritated by the slowdown- things would have seemed rushed otherwise. It's odd that shows like this and 24, which want to only have one tightly-scripted season, constantly get renewed. Most other shows what to go on forever and get cancelled quickly. Makes me think the public actually does want something original, after all....
Also: I love the character of Samson, and I think that it's great that Michael Anderson got this role. He's a great actor, but of course always gets relegated to sterotypical Hollywood roles due to physical stature. Now he's really got a chance to shine, and he's definately earned it.