Automatic Progression: Because of the lack of crafters and most spell components, we will use the automatic progression rules found here.
Hero Points: The hero point system will be used. Hero points can be gained in game for role-playing, and in the bonds of friendship section there's a mechanism to gain hero points if the relationship between PCs has lowered.
Combined Skill Checks: There are some instances where a combined check will be called upon. In this case, there will be a primary skill and a secondary skill. You would roll a number of dice equal to the secondary skill's ranks (min 1), but using the modifier of the primary skill, and be looking for # of successes. More successes could mean a better success.
For example, when rolling to see through disguise, you could roll Primary (perception) and Secondary (knowledge local- for humans). If you have +5 to perception and 3 ranks of knowledge local, you'd roll 3 perception checks, each at +5, the DC based on the opponent's disguise roll. 1 success and you might see that they are disguised, while more successes might indicate that you can identify what they really look like.
Sometimes these skill checks will be opposed. In this case either one person could set the DC against the other (such as the above example with disguise) or both could roll NET successes, such as if two people were trying to convince someone to take contrary actions using diplomacy. In this case the DC would be set (not necessarily the same for both people) and the degree of success would be based on who had more successes than the other.
This would be used for things that are more complicated than standard skill checks, such as for a chase scene, or a difficult negotiation. For most skill checks, the standard uses would apply.
Group Skill Rolls: For some skills, like stealth, one person can ruin it for the party. If the party takes 10 minutes to prepare, and they are going together (helping each other), they can make a group skill roll. In this case, the results of everyone's skill is averaged together as is everyone's result. (So stealth rolls of 20, 15, and 5 would be a 13 for everyone). This would mean everyone gets seen, so a high stealth character only stays hidden if he is separate from the group. Characters with -4 or less friendship cannot participate in group rolls together (this is kind of like aiding another).
Alignment: Unless required by your class (like paladins) everyone starts as True Neutral. Your alignment will be determined by the DM based on your actions in play. This alignment is only revealed by the way you respond to spells (such as detect spells). Keep in mind, unless you are a cleric, your alignment will not likely be detectable until higher levels.
Bonds of Friendship: Without civilization and law, the family structure means more than ever. Even with people you disagree with from an alignment perspective, the sense of trust between party members is important.
Some things can improve trust: such as sharing an intimate secret, protecting a friend in combat, rescuing a friend, etc.
Some things can lower trust: abandoning a friend, keeping secrets or telling lies, acting selfishly.
Having a high level of trust can provide various benefits, such as an improved aid another bonus, hero points you can use to assist each other, or temporary teamwork feat benefits between party members. See the Bonds of Friendship Post.
Religion: Most of the large churches were destroyed, and as communication between cities degraded, the religions splintered. Druids, Rangers, Oracles, Adepts, and Shamans are unaffected.
Paladins serve the ideal of Lawful Good rather than a deity. Clerics, Omdura, and Inquisitors must "Create" a deity- choose their favored weapon, alignment, and domains. You worship them as a "small god" and may be their only follower- but with so fewer humanoids around, there is more "faith" to go around. Your god functions just fine with you as his likely only follower.
Magical Components: Spellcasting components are extremely hard to come by and can't be just "purchased". Spellcasters are encouraged to take Eschew Materials. Having a spell component pouch is not a free pass on this. However, there is a feat called Blood Magic which downgrades the Blood Money spell to a cantrip. False Focus is also a good spell for those with a religion.
This also affects magical crafting feats (such as scribe scroll) as the materials becomes extremely hard to come by. Any magical item being crafted is likely to require some kind of quest to get the materials. These feats are discouraged.
Classes: While any class is allowed, some are clearly at a disadvantage in the new world. Spellcasters will find many spell components hard to find, and foci are difficult to replace. Quality items made of metal are hard to come by, so replacing broken weapons can become a chore, as can replenishing arrows or bullets. Spellbook ink and new pages and books are hard to aquire, favoring sorcerers and witches over wizards and arcanists.
Classes with pets (familiars, eidolons, animal companions) are at an advantage with the extra action economy, though arcane casters are still viewed with distrust.
Social skills are still important, as there are other intelligent species, but classes that rely on societal institutions, like the investigator, or certain bard/rogue builds might find themselves with less to do. Meanwhile, classes that are comfortable in the wilderness (ranger/druid/hunter) or classes that rely on their wits (rogues), or classes that can get by with minimal equipment (monks/shifters/brawlers) are at an advantage here.