What are the differences between D&D 3.5e and Pathfinder, on the DM's side?

Question

The very similar question here has answers that focus a lot on the experience of the players.

As a fresh PF DM who was used to 3.5e I'm more interested in changes to rules that I need to pay attention to after I'm already sure that my players know their class and I know the classes of my NPCs. (Unfortunatley this didn't prevent me from not noticing the stealth errata to unchained rogue's Sneak Attack but let's not talk about class features anymore.)

I'm interested in things such as "Acrobatic checks to move past enemies now check against CMD instead of using a fixed DC", the obvious "combat maneuvers now work really differently" (but that was easiest to spot) and especially any subtle rule change in skill adjudication, resting and mundane healing mechanics.

Basiaclly, things that I'd better know if I want to get the rules right instead of defaulting to the well known 3.5e rule that has been changed without me noticing.

A vague collection (i.e. look at the rules for extingushing a fire) will be enough. I will appreciate answers that provide deeper details but they will not be valued more. I can browse the SRD.

I'm not interested in spells that changed (I will read all spells before using them), skill points being gained differently or in new class features and other things that belong to character building, including the different XP system.

Since the scope of a game like Pathfinder is really vast, I'm asking you to focus on core rules. I won't bite if you mention some other big or famous changes, but the answers won't be evaluated on those.

Answer 1

That is a pretty long list, but I will keep this focused on things in the Core Rulebook and Bestiary only:

• Afflictions changed, especially how Poisons work. They still apply ability damage for most poisons, but their damage got reduced and spread through several checks through several rounds. Multiple exposures to poison will increase the duration and DC to remove it from your system. Diseases work mostly the same way, but are presented slightly better;
• Ability Drain and Damage work differently, damage being temporary and healed with rest, and drain being permanent and removed with magic. Damage will apply a -1 penalty to all checks related to that ability for every two points of ability damage, and drain will reduce that ability directly. To elaborate on this, you only take the penalties from ability damage for every 2 points of damage taken, while in 3.5 it affected you right away if you had an even (12, 14, 16, etc) ability score. Example, going down from (ex) 16 to 15 would reduce your ability bonus from +3 to +2. That only happens with ability drain now. Ability damage doesn't directly reduce your ability score but apply a penalty. So, many related stats are unaffected by ability damage, such as the number of bonus spell slots (Ex: high Int as a wizard), the DC from class abilities (ex: Domain powers), the requirement for feats (ex: Str 13 for *Power Attack), etc;
• We have mostly the same Conditions, and many rules will refer to one condition or another, and some of them are slighly different from 3.5, some got removed and some got promoted to being a condition now, so keeping those in hand (available in the GM screen) will help a lot;
• There is no permanent Level Drain anymore, abilities that Drain Energy will either be temporary or permanent, but even if permanent, they can be cured with magic;
• Several Combat Maneuvers work differently now. While disarm, sunder and trip can be used instead of a melee attack, the others are Standard actions. Pay close attention to how Grapple and grab interact, a creature with grap will make a Grapple CMB check against the target's CMD everytime it lands an attack. This is important because a lot of creatures have grab;
• Experience Distribution changed slightly. Characters will level up quicker at the first 5 levels, the number of XP needed for each level and how much XP is award per encounter is different. Note also that now you simply compare the total XP of all creatures in the encounter to an encounter with a single creature, that is the CR of that encounter. And there is no diminishing returns on XP as you gain levels, you simply need more XP to level up. Example: two CR 2 creatures (600 XP each) would be equivalent to a CR 4 encounter (1200 total XP). Calculating the CR of NPCs with class levels is also different, but nothing that can't be fixed by using existing NPC stat blocks;
• Regeneration is now turned off for an entire round when the creature takes damage from a source that bypass their regeneration, so you no longer need to track lethal and non-lethal damage on a creature with regeneration. Also, effects that cause instant death will no longer prevent a creature from regenerating, you must also deactivate their regeneration for it to work;
• Many combat-focused feats changed, so it's worth checking the feats the players and monsters use. Commonly mistaken feats are Power Attack, Dodge and Cleave. Power attack now scales every 4 levels, granting a fixed penalty to attacks (-1) and a fixed bonus to damage (+2 for 1h and +3 for 2h). Dodge is a flat dodge bonus to AC, which is only lost if you lose your Dex to AC, and you no longer have to designate dodge targets. And Cleave is a standard action to attack a second adjacent creature if you hit the first (old cleave is now Cleaving Finish);
• The Track feat is gone, so you may track creatures using Scent simply by making Survival checks. This is especially useful at lower levels, where animal encounters are common;
• Using the Heal skill, when Treating Disease and Poison, you no longer use the healer's check result instead of your own, but gain a +4 to your check if the healer's check beat the save DC. The skill may also be used to Treat Deadly Wounds (DC 20) when using a medkit, which may recover hit points, adding your Wisdom modifier if you beat the DC by 5 or more;
• Since Detect Magic is a cantrip, players can easily identify magic items by making Spellcraft checks (DC 15 + item's Caster Level). The Identify spell is still useful to identify cursed items and (mostly) prevents you from failing to identify magic items. So, expect players to immediately identify (and then use) most magic items they find, especially if they Aid on that check;
• If you run any published campaign or adventure, read and understand Haunts (they are like supernatural ghost traps). They are very common and even at early levels (to prepare the GM and players), and aren't difficult to grasp, but may take time during the game as you read their mechanics;
• The rules of Polymorphing changed drastically, though this is briefly mentioned on the druid changes on the player side, it is worth reading those rules and making sure you understand their impact. But to sum it up, you no longer become that creature, you take their apperance and some of their abilities (not all of them), listed on the ability that granted you the polymorph effect. Your creature type does not change (a human druid is still Humanoid, you cannot be under two polymorph effects at the same time, and you lose all your original form's supernatural and extraordinary abilities.

Answer 2

Adding more DM-focused points:

• The creature types are different. For example, there are no longer Giant and Elemental types (who are now subtypes). Also the statistics are different. For example Monstrous Humanoid have d8 HD in 3.5 and d10 HD in PF.
• Undead are d8 and get Cha to hitpoints and other con-related stuff.
• Level adjustments and LA-buyoff are eliminated in favour of simpler rules based on CR.
• Many iconic monsters are changed from their 3.5 counterparts, in subtle and sometimes weird ways. Dragons are an easy example.
• No beholders... for reasons. Legal reasons. :)

Gotchas:

• Tumble works differently. I uses opponent CMD, not a flat check. Makes AoOs work vastly differently.
• Skill system is completely revamped (much better IMO). No synergy bonuses either.
• Skill points from intelligence work retroactively. I.e. you always have your class + int modifier skill points to distribute.
• PF traits are not like 3.5 traits. PF: One good positive effect. 3.5: 1 minor positive and 1 minor negative effect.
• Because of the combat maneuver system, the size difference between grapplers matters less. I.e. your players will not automatically lose when grappling larger creatures.
• Level drain was mentioned, but Paizo basically removed all manner of de-leveling. Among other things this includes XP costs for things (spells, item creation, etc).
• No ability bonus stacking.
• Mind-blank is not blanket [Mind-affecting] immunity. Just a bonus. A typed one even - resistance (what were they thinking?).

On a less specific note:

• They eliminated all manner of loops and exploits, or simply didn't inherit a ton from the myriad 3.5 splats.