Ethan is here on purpose
Ethan has volunteered for a process to help him get over a trauma that happened in his line of work. It is highly secret and dubiously ethical, and involves kidnapping people and uploading their consciousness into a virtual reality - hence why Kate has been there for 12 years when he only saw her 5 weeks ago, time runs differently Wayward Pines is the sister city of The Village.
A quiet, idealistic town with lots of Sinister Surveillance that's cut off from the outside world. Maybe it's even protected by a sentient weather balloon. Sheriff Pope is an Eldritch Abomination and Wayward Pines is a secret government project built to contain him/it.
That's why so many people in s1e3 keep saying that Wayward Pines needs a good man like Ethan. They believe that he's the only one able to resist the corrupting influence of Eldritch Pope & defeat it.- I may be half wrong about this one. It looks like there IS an Eldritch Abomination, but Sheriff Pope might not be it being possibly dead and all.
- May not also be so because in an ironic twist, his body was eaten by the real monstrosities that the fence is keeping out of the town.
The so-called "real world" is a Matrix type illusion and Wayward Pines is real.
The world is really full of horrible Eldritch Abomination style monsters that like to eat people but which also run towns like Wayward Pines where humans are allowed to live out their lives in peace provided that they follow the rules. Wayward Pines is a prototype of Panem.
Complete control of a fenced in community, desensitizing the populous to violence, "wolves" that I'm pretty sure arn't wolves. Wayward Pines actually takes place 20 Minutes into the Future.
Most of the people have been in the town for an indeterminate amount of time, with one having been in since 1999 and insisting it's been only a year, and another has been there a few weeks and has experienced (and aged) 14 years. The town is surrounded by an advanced electric fence which may or may not be blocking out all outside signals, with at least one advanced looking warehouse attached and filled with the cars and belongings of the townsfolk before they arrived, most of which are coated in thick dust, including Teresa Burke's car, which logically should have only been sitting for a couple days at most. Much of the technology and equipment connected to this seems relatively advanced (universal surveillance, files using thin metal containers and a "futuristic" font, those things just outside the gate). Either the townsfolk are being subjected to a strange form of Time Dilation which effects some people more than others, or they have been held in stasis for variable lengths of time and are only being released when the time is right. This adds some questions as to how Sheriff Pope and Nurse Pam can exist on both the inside and outside, but it could simply be that they are clones, or perhaps Really 700 Years Old. In essence, Wayward Pines is the sister city to a different village. Wayward Pines is the past of the Flintstones-verse.
Assuming that the Flintstones is not prehistoric but post-apocalyptic, it would take place after humans have re-expanded beyond what the stored supplies of Wayward Pines can support and attempted to reconstruct the modern lifestyle using whatever fell to hand. The Government is involved with how the world got the way it did.
I'm pretty sure the drastic change from human to aberration couldn't have happened over 2000 years. It looks like it happened over night, around 2095 or so. Also, I'm sure people would have noticed aberrations running around slaughtering everything in sight over the years. The aberrations would have had to have been developed in secret, say as a Government Super-Soldier project Gone Horribly Wrong, and accidentally released them all, overrunning the world.- This almost has to be true for the above listed reasons but also Abbies are not described as immortal or invincible. Just really tough. So unless something else like a virus a 'la Plant of the Apes helped take down humanity or the Abbies are the result of people infected by it, it wouldn't have gotten this bad. A chopper and a minigun, a Humm V and .50 Cal or a tank would all make short work of those beasts.
Wayward Pines is actually an alternate dimension. One that someone/something wants humanity on.
Think about it, time clearly flows differently there and seems to be somewhat selective. If five weeks outside equaled ten years inside then 3.5 days equals a year. Yet Ethan's family doesn't show up weeks or months later. The time inside and out seem to have been synced at least during the time they were separated. An nearly impossible disaster wiped out humanity. The current evidence seems to suggest you cannot get out of Wayward on foot but Sheriff Pope can drive out to pick up new arrivals. Someone or something is actively seeding this planet and the Abbies like came in from another alternate dimension instead of the completely implausible story that they evolved.- Time isn't messed up, actually. It's the order in which the hibernating humans are awakened that varies. Kate experienced 12 years in the town because Pilcher's people revived her 12 years earlier than they revived Ethan. Ethan's family didn't experience such a time-lag, because once the people running things decided that he wouldn't stop escaping so long as he believed his wife and son were out there somewhere, they gave him his family back immediately as an anchor to the town.
Wayward Pines is the backstory to Attack on Titan
Spoilers for anyone who hasn't watched Episode 5: The abbies will eventually evolve into Titans, and Wayward Pines will eventually grown into the city behind the walls. When everyone eventually learns the truth about Wayward Pines most of them...will grudgingly accept it and go on with their lives.
The first group was told the truth immediately, and missed their home. Many of these people have been living in Wayward Pines for over a decade so no matter how oppressed they may feel, it has basically become their home. Wayward Pines is the backstory to Tengen Toppa Gurren Lagann
The abbies are the prototype beastmen used to keep humanity in check. The final scene was a a nightmare.
Reconquering and rebuilding should not have been NEARLY that easy, especially after most of the behind-the-scenes people had turned on Pilcher. Most of the adult survivors were sterile.
The settlement is about twenty years old by the time Ethan wakes up, but there are apparently few children being born during this time and it's enough of an issue that couples have regular "fertility counseling." In Season 2 babies and toddlers are everywhere, having been born to the (extremely young) parents in droves. The current teenage and adolescent parents were all very young children at the time they went into stasis, too young perhaps to have been affected by one of the many biological agents floating around as the world ended; their parents weren't so lucky, which is why so much emphasis was placed on the kids and teens being the First Generation— They weren't the first generation to live in Wayward Pines or the first to be born in it, but the first who could reliably produce offspring for Wayward Pines. Something about the stasis process induces sterility.
Explaining why relatively few children were born until very recently; maybe the stasis is more likely to cause infertility the older you are when you undergo it, which is why those who were children upon being "frozen" were less affected and able to produce more offspring. This may also have something to do with why Jason and Kerry haven't had children yet: It seems as if Jason was very young (an infant?) when he went into stasis, maybe there's a certain age-range where you're probably "safe" and Jason was on the too-young side of the scale, just as most adults were on the too-old side.