If everyone was in some sort of stasis tubes, the whole interior of the base could have been flooded with Nitrogen to prevent any decay and kill anything that managed to get inside during the time they were 'sleeping'. Also, as some folks pointed out they government may have been continuing to update their technology…

Maybe they have more advanced tech still hidden away that will be available for the 'First Generation' to use. Since the truth will apparently cause any of the unwilling adult 'volunteers' to self-destruct, they could be hiding all the ultra-tech stuff for the same reason.

No, there's no time travel. All the scenes that occurred outside of Wayward Pines were in the past. The way they cut back and forth just made it seem like they were happening at the same time. Pilcher and the original Police Chief both joined all the 'unwilling volunteers' in the stasis for the 2000 years sometime…

Okay, nice twist and I admire the way that the scenes outside of Wayward Pines in the earlier episodes seemed to mesh with the events inside WP, giving the illusion that they were happening at the same time. However, logically if they had the entire Burke family 'on ice' for 2000 years, why not 'release' them from…