Honestly a show with this kind of idea is best done to me in mini-series format. Something that should be on HBO or Netflix where shows don't have time lengths. But you get like Ten 60 minute episodes to do a series.
Falling Skies fell into a trap that I see many shows fall into.... they have a good idea for the start of a story but have no idea where it should go.
So many shows struggle just to get picked up for a first season they don't work hard on a long term story.... then they do well and they get renewed and the writers go "Oh shit oh shit oh shit we need to take this story somewhere" and then they scramble to take it somewhere and often wind up on a story arc that they are stuck with.
I think this is why so many shows now are based on books.... you know it is a good story and you dont have to guess where it should go in seasons beyond season 1.
LOST felt like this in season 2... lol like the writers went "Holy fuk people are actually watching this?"