Another thought:
How could the scientist know that humans would mutate 85 years in the future, unless he somehow caused it himself? It could be that he releases some kind of "I Am Legend" virus just before freezing himself.
Here's what I'm thinking of:
-Some time before 1999 the Scientist starts selecting people to build a future "master race". Kind of like the villain in "Moonraker".
-He gets a conspiracy of people working for him (including the Secret Service, the Nurse, and Terrance Howard) to start capturing and freezing the candidates in hibernation tubes in the Wayward Pines "Ark".
-It takes at least 15 years to get enough people to fill up the cryo tubes, so the first batch of people haven't aged since 1999.
-The freeze a lot more people than they plan to wake up any given moment, so they have lots of "spares" to wake up if someone dies.
-Ethan's wife was getting too close to finding the facility, so instead of killing her they froze her and her son.
-Once all of the hibernation tubes are full, the scientist releases a "mutation" virus and freezes himself, the Nurse, Terrance Howard, and the rest of the conspiracy.
-The virus doesn't take effect immediately, but by the year 2100 it has caused a Zombie Apocalypse that destroys the world.
-The scientist and the other conspirators wake themselves up first from the Ark and build Wayward Pines into a town inside of the existing electric fence.
-The start unfreezing enough people to populate the town. But they don't unfreeze people in the order that they were frozen, so you have people frozen in 1999 waking up at the same time as people frozen in 2015. Whenever someone in the town dies, they unfreeze someone else to take his place.
-The keep the adults in the town, but the brainwash the kids into a cult, give them the cure/weapons to fight the monsters, and use them to repopulate the world with the Scientist as dictator and cult leader.
There's no actual backward time travel at all, just hibernation tubes.
