I agree that the shows ending was a let-down and filled with plot holes compared to the book series.
BOOK SPOILERS
In the book, Ethan and co get to the mountain base and realizing they can't fight off the abbies, choose to all freeze themselves and wake themselves up again in the future where the abbies are ideally gone or in hibernation. The situation is still dire since the community is running out of food so freezing and escaping the abbies into the future is a last measure. The book ends with Ethan waking up in a new world.
One major problem I had with the tv show was the kids taking control in the end. Unless it was a hallucination, how did they do it? Abbies are supposed to be tough and can wipe out trained soldiers. I truly doubt a bunch of kids who have minimal training, let alone army training and military strategy, could rote the abbies from their base and rebuild the wall. Based on the education received, it seems the children were focused more on understanding Piltcher's theory and there is little evidence to show that they gained real practical skills to maintain the community.
I dont dislike Ethan's sacrifice in the show actually. It was stupid but symbolic. Ethan, the "traitor" of Wayward Pines, sacrifices himself for the survival of the community and stays back to protect the people, truly being the man needed to protect humanity. Pilthcer, the "savior" was the cause of humanity's destruction, shutting down the power of the wall and thus leaving them to die and is shot for his efforts. I think the show could have ended bittersweet with the people freezing themselves as abbies approach the capsules, implying their death, or sticking with the original with Kate waking up in a new distant future. I was really disappointed after episode 4 with the reveal that the world was in the future.