Melissa Leo is certainly a great villain but the sheriff is key. If they don't bring back TH, what they should do is have Ethan turn out evil somehow via hypnosis.
A great twist would be to have TH come back as an amnesia ridden car accident victim who turns out as the hero. Maybe WP could be a scenario being played out on an Xbox from another dimension.
All we may end up being are game pieces in some alien's toy box. We could merely be toys like the diorama as depicted in the show's opening.
More pedestrian theory:
IF we want to keep this all in the US government conspiracy thing and leave out other universes, worm holes, and time travel and just have good old aliens, then my next guess is the the Secret Service, who do a lot of undefined things besides protecting the president, are then in on some nasty experiments. Toby Jones, the friendly town doctor, is the go-between between the aliens and the Secret Service.
I didn't read any spoilers or books but just conjecture, but here's what I think could happen regarding secret service. A long time ago they got control over the events of Roswell and got some aliens. They were allowed to live in selected cities and towns. Unlike Men in Black where aliens on earth only live in Manhattan, the Roswell aliens live in out of the way small towns like Wayward Pines.
Being similar to humans and having all the same faults and power struggles, the aliens in Wayward Pines are most recently up to to abducting people for various reasons. Like the TV series V, there are good aliens and bad aliens, and there are good people and bad people and lots of alliances involved.
If this series is just for a year, then humans get to escape, but if show goes on, then people (and aliens) switch sides and the line between good guys and bad guys gets blurred. I may be taking too much from the show V, but most concepts like this, especially M. Night, are derivative and harken back to Twilight Zone episodes.
There's nothing wrong with that, but what counts is how well the story is told.
