I think this setting feels like its trying to do too much all at once. The concept of aliens reshaping the planet, followed by seeding with alien races and cross-breeding genetics, followed by the "mystery" of their disappearance, followed by the paranoid "zookeeper" and the strong focus on Central IL areas, etc, etc, is just a bit much. I am also not certain that if Chicago were underwater that central IL or even most of the Midwest would not be the same, but I suppose that's neither here nor there in a fantasy game.
I like the originality here, as this game does seem to have a great breadth of variability in the game you can choose to play with it - the political intrigue of being a PSH who is leading his enclave to decide whom of the NH's you can trust, etc; the hack-and-slash GURPS style you can find wandering the "wastelands" of the Heartland; even the global mysteries of the keepers and their true intentions for this world.
I am somewhat inspired by this concept, but like my first paragraph states, I am also not sure what to utilize or leave out given the mish-mash of ways you could take this setting. I think I want something a bit more clear and limiting to begin with. Leave the ideas of the zookeepers and the paranoid army stuff for expansions. Give them the basic start from the mystery of the keepers leaving and no one truly knowing why they came at all thing, something like that. That's a bit more clear and easier to begin with.
The quality of writing is not so great, very in-depth on some thoughts when it comes to points for flaws/feats and what the tribal culture of certain groups are, but not so clear at many other times nor as well expressed. Could definitely use some editing. The idea I mostly get from it is "I want players to be able to make up their own kind of game", and while I get that, I really think I want to start off a game setting with a better definition of what we're trying to do.

Comments
Pueblo Colorado
During the first part of the “restructuring” large percentage of the population was removed. Those that were left formed quickly into communities that often survive even unto this day. The second phase was the alteration of the atmosphere which increased the average temperature to the point of melting the ice caps and making large tracks of lands hospitable for occupation (Siberia, Arctic, Northern Canada). Stage three was the introduction of neo-humans and “combined” creatures (wolfen, raptors, etc.) Combined refers to the genetic combining of two different creators to get the desired traits. Humans combine with animals were able to produce intelligent species (with varying degrees of intelligence) that still retained the survival traits of that particular animal. The last stage was the introduction of alien species, both plant and animal.
A Pure Strain Human Colony quickly formed in Pueblo, Colorado. The desolation of the cities made the choosing of a city rather difficult but the early Pioneers choose this city as it had access to a lake. With an initial population of around 10,000 people the quickly got many of the services running. There was plenty of material to with Pueblo itself that most of the effort was to get this city back to being fully functional. However with progressive stages the population realized that the “game” had changed and with the sighting of strange creatures and people they needed to set up proper defenses. Walls were built, militia trained, defenses erected, outposts manned the city quickly shaped up. With the lake and farm grounds this city, within its zone of control, is able to be self sustaining. Initially the city was in contact with other human settlements but with the rapid changes in environment, the introduction of strange creatures and races, the deterioration of roads, communication, at least with face to face stopped. The only means of contact was via short-wave radio. Over the decades fewer and fewer cities kept up communication. There is uncertainty if the cities were overrun or that they simply used up all their spare parts. Whatever the reason, the further isolation further feeds the paranoia.
In the beginning of the restoration it was almost universally believed that they were living the Tribulation as described in the Bible. The rapture followed by horrible geological and climatic events was enough to cause even the staunchest atheists to believe they were seeing the 2nd coming of Christ. However, after time, that form of thinking started loosing sway over the population and other thoughts and explanations have occurred.
There are various factions within the city:
The Zionists: (religious) – they believe that the human race (proper) is chosen by God. It is their purpose to live a separated life from the other races to prove their devotion until God chooses to allow them to join the rest of the humans taken. They recognize that fact that the neo-men are in fact modified human beings, but have determined that they were changed as judgment against them, not unlike some beliefs regarding blacks bearing the sin of Ham. They feel that while they themselves are under judgment, they are still capable of being restored into favor and retrieved by God.
The Zionists (secular) – they seek to maintain the knowledge and skills of the ancients in hopes of one day being able to exert rule once again. For various reasons, while they have maintained the life and the knowledge, their goals of asserting the human race still remains a faint dream. The low birth rates combined with the brutal distances separating human settlements makes it very difficult to become the conquerors they would like to be.
Followers of the Way (religious) – realizing that their previous understanding (as Zionists) was wrong they have come to believe that the world has hit a new Aeon and that God will redeem them in a way different than shown in the two Testaments. They await a prophet to show them the correct path. They ponder the necessity of sharing their faith with the non-humans. To date, this has (mostly) been academic as it has not been determined if the non-PSH even have souls. The Followers hold to the basic tenets of love for others, and temperance.
Progressivists (secular) – A small but growing group that wants to work with the other races, explore new territory get beyond the fortress mentality. It members not only include members of academia but also some Followers of the Way. Their influence is growing, but is currently insignificant. The Zionists, who are in charge, seek ways to pacify, stall and thwart the Progressivists whenever possible.
Regarding the post
This is rather rough as I just copy and pasted from the forums that I originally posted (www.herogames.com search "beta world" )
This was written with the Hero System in mind but that does not mean that the final product will be in that system.
Some things need to change as terms are taken from existing games.