SETTING:For the setting of this game, I would select a specific region and leverage the available maps to really flesh out the damage done during the apocalyptic event. I would keep the area limited so that I could breath real life into it, instead of making the entire state (or country) a sandbox.
CRITTERS:I think I would develop an effect or exposure that sets your monsters apart from the standard PFRPG. Like a radiation or a toxicity template. Also, I'd create some weird or alien effect that boosts the intelligence of critters that normally are not.

You might want to consider allowing
Psionics. It certainly fits with the feel of the game. I like what the Dreamscarred folks have done with Psionic rules for PF.
Good Luck!