This past week I spent some time working on the first adventure of my new Pathfinder campaign. I am working on making combat encounters (my favourite part of building a campaign!) and ran into some roadblocks. The biggest problem with monsters is that their stats are so interconnected: A monster's Hit Dice determine its saving throws, attack bonus, and HP as well as immunities to various effects. Its Constitution determines its HP and Fortitude saving throw. So if I want to make sure my monster has enough HP to survive a few rounds against the players I need to jack up its Hit Dice or its Con or both. Either way though I end up giving it a massive Fortitude saving throw which means that any spell the players throw at it with a Fortitude save cannot succeed. This is a real mess. I don't want giving a monster high HP to mean that it is immune to many classes of spells! The other problem with stacking on more Hit Dice is that my monster would also have a extremely high attack bonus, quite probably making the character's Armor Classes irrelevant. Ack! If all of the monster's stats weren't so interconnected I could simply assign reasonable values to each stat and it would be grand but with the current system that isn't possible.
I can kludge things, of course. Normally monsters get to roll a single 8 sided die for HP for every Hit Die they have. Instead of a d8 though I can simply give my monster a d40 and it will suddenly have plenty of HP... but the players will be very confused when their opponents' stats don't make any sense. Eventually it will become clear that the monsters aren't built on anything like the same rules system as the players and people tend to dislike that. Quite understandably they like immersion and feeling like the playing field is level and randomly kludging stats can ruin that. When given a choice between using the default monsters which have awful stat layouts which generate stupid fights and kludging I will kludge every time but I wish I was not put in that position.
The second issue I have had is trying to build a fight that has ~8 normal humans in it. If the players decide to wipe out the little village they are going to visit then they will run into some opposition but the nature of the opposition is limited by the rules surrounding weapon damage. A battleaxe or longsword hits for d8 damage which means that any scrub with a weapon has to hit for 4.5 damage on average. The difficulty with this is that I can't have the players fight 8 dorks - if the dorks go first they stand a good chance of wiping the party out before any of the party members gets an action! On the other hand if the players go first the dorks have so few HP that the players could easily kill nearly all the dorks before the dorks get an action! It is difficult to get around this dilemma because aside from having all of the enemies have terrible Strength scores (your whole militia is a bunch of wimps? wut?) or having all the enemies use daggers (your militia is armed with daggers? wut?) you just can't get base damage down low enough to make having a large number of opponents reasonable. Again, it 'makes sense' that a longsword does a particular amount of damage but it means that I really can't make particular fights work the way I want. I don't want to kludge in a rule that these particular militia folk have a -50% Sky Is Cheating damage penalty but that might be the only way to make it work right.
Pathfinder does have the old DnD tradition of having lots of things constraining monster design because they 'make sense' but this is a real problem when trying to design really interesting, intense fights. When fights get hard and design gets elegant the clumsiness and ugliness of the base systems really gets brought to the forefront; we know this from any number of games that had awful design at the start and had to clean up their systems when hard content was added in. WOW is the best example I know of but Magic: The Gathering, Diablo 2&3 and others show us that when you want to add high level PvP or serious challenges you often end up wishing the base systems supported those properly instead of being 'realistic'.