A classic setting of fantasy and adventure, the magical apocalypse can be extremely difficult to get right. The difficulty lies in the way that an apocalypse challenges the assumptions that everyone normally has. In any game, players have certain needs; in Pathfinder, they need to shop for magic items, sell their loot, and rest to regain spells.
However, the point of designing an apocalyptic setting is to challenge the assumptions of a normal world. A player needs to feel that things are drastically different, and the best way to achieve that sense of loss is to do away with the perks of civilization. However, at the same time, a setting can’t be so frustrating and difficult that no one wants to play.
Unfortunately, most apocalyptic settings tend to fall to the other extreme and make most amenities available in some form, only using the apocalyptic setting to justify new powers and abilities. This often makes the characters into unstoppable badasses roaming the landscape as they please, since the rest of the world has been hit harder by the end of days. This kind of thing can be fun in its own right, but doesn’t really accomplish the goal of a world-ending setting.
To achieve the right feel, you have to make frustration work for you instead of against you. Make limitations, but make things available. Instead of a magic shop, there’s a mad old peddler with cracked teeth; he sure as beans won’t have the selection of one of the old magic emporiums, but every now and then he’ll have some unusual, crazy-strong item that someone really wants. Let the players feel like they got a little something in return for everything the apocalypse took away. Let the players feel like badasses only in comparison to their bleak surroundings.
The manner of the apocalypse might well affect the characters’ options. If it was an arcane explosion, perhaps some magically protected locations survived. If a flood, or divine fire, or icy doom befell the world, then certain creatures may have survived; the point is to remember that anything that survives the apocalypse becomes much more important as a result.
Perhaps that’s how the characters become heroes.