I enjoyed the first 2 seasons of this show and think the premise is generally interesting. However, I think the writers are having a difficult time communicating their vision or, like many shows with great premises, are making it up as they go along. Below I detail what are some of the problems dragging down the generally good dialogue and good individual episodes. If you can look past the problems in the story arcs, the majority of episodes remain very good if you don't think about it.
So, in this season we learn that in the future there is technology of such an amazing degree that they can send people back in time regularly and have the ability to give humans amazing and important super powers, but they can't solve their own meager problems. We don't know what future catastrophe they are trying to evade (but in one episode we find that an amazing leap in our level of scientific knowledge may help), but we know the dystopia they face is a world with one city that is powerful and "ok" with walls keeping out the rest who presumably are not so well off. We don't know who sent back the 4400, or Isabelle (who has a mission to eradicate the 4400s). Was it is the city or those out of the city? If its those outside the city, the plot makes no sense since that means they have this incredible technology and aren't using it, if it is the city why don't they just start helping the people outside the walls? I think we are supposed to believe the city is evil and hoarding all the resources (except world changing technology...), and those outside the city are trying to avert the current state. But, its not clear yet and it does not need to be clear. If it ever is it might make sense, but I'm really starting to doubt it.
So, problems like this are nagging at the show, and I don't get the feeling that the writers have good coherent answers after this season.
The show also has occasional religious overtones, which are amusing but mostly embarrassing. I confess that if someone had the power to heal we would no doubt revere that person and possibly worship them...unless we knew how they did it. We admire science but don't worship it. In this show every person who watches the news now knows that the 4400s have their powers due to specific generally understood scientific reasons. It would make as much sense to worship the iPhone or your doctor when they give you antibiotics as to revere the 4400. The fact that the writers can't make this distinction between science, religion, and the supernatural is awkward.
Mia. Mia can see the future. This ruins about 80% of the plot episodes, if they acknowledged it. But they don't, but we know she can so it really is always an ever present plot hole. During this season Mia supposedly even gets so she can control her ability, making many of the dilemmas even more ridiculous.
Isabelle. Supposedly Isabelle is a super genius based on the first few episodes but devolves into someone with the mind of a 10 year old that is always making sub-par decisions. I like her role on the show, and personally since I have decided the 4400 are the catastrophe root for her to destroy them all, but her being a genius one episode and then a dimwit for most of the season is tiresome and disrespectful to the audience.
There are other problems of course. The amorality of Collier, the dramatic personality change of the neuroscientist on the show, and the useless end result produced by Colliers big plan. So, now there will be 11,000 "4400s" instead of 4400? Hmmm....why does that matter? Why didn't the future people just send back 10,000 to start with and save all the internecine fighting?
Despite these complaints, I will continue to follow the show and think it still beats many things out there. But it always saddens me when the wheels come off a potentially fantastic chassis.