The Creatures

In the years since the flash, humanoid civilization has been overrun by other creatures: 

Illithids: The Mind Flayers have taken over large areas of the underdark as well as the ruins of some cities above ground. They are always on the hunt for humanoids for work as slaves or meals

Beholders: The Eye Tyrants disintegrated out areas that once belonged to the dwarves. Their slow flight speed leaves them most at home underground, though there are some who have taken over mountainous regions.

Dragons: Dragons have flourished with the reduction in humanoids. While some are good- they are distrustful of mankind. Most hoard historical artifacts from the lost world and wealth recovered from cities. Some metallic dragons rule over cities, though humanoids don't enjoy equal rights as dragonkind. 

The Undead: The cataclysm left many cities demolished and most of the inhabitants dead, but some necromancers were able to avoid their fate by becoming undead- vampires, liches, ghosts, or ghouls are among the most common. There are necropolises that are similar enough to former cities- though the living are likely not to be welcomed.

The Fey: After some years, without humanoids to encroach upon it, the wilderness began to thrive. Animals and magical beasts repopulated, and there was an increase in fey. The lack of cold iron and civilization to keep them in check has enhanced an already chaotic species.

Living Spells- During the Flash, areas of high magical concentration and powerful spell books overloaded with magic, and living versions of the spells roamed the areas. 

Outsiders- Strangely enough, with the reduction in humanoids, outsiders have shown less of an interest in the plane. Perhaps both the good and the evil ones were drawn by mankind's faith? In any case, fewer and fewer outsiders have been encountered since the flash.

Changes to the "Favored Enemy" Class Feature:

Aberrations: Splits to Aberrations(Beholders), Aberrations(Illithids) and Aberrations(Other)

Outsiders: Combined into "Outsiders" (no need to select a subtype)

Dragons: Split to Dragons (Metallic), Dragons (Chromatic), and Dragons (Other)

Add: Living Spells (new type). Living spells are separate from the "ooze" category. 

Humanoids: Some classes of humanoids are combined

• Humanoid(Demihumans) combines Humans, Elves, Gnomes, Dwarves, Halflings, Half-Elves, and Half-Orcs. 
• Humanoid(Monstrous) is Orcs, Half-Orcs, Goblins, Gnolls, Kobolds, Hobgoblins.
• Humanoid(Chimeric) is Tengu, Catfolk, Ratfolk, Grippli, Vanara, Merfolk
• Humanoid(Giant) remains largely unchanged.