It's a bit amusing that you are complaining about this, as 3e which Pathfinder is based on had the exact same bonuses. I do find it weird you never ran into the same thing there. 4e does a better job at making the character building a bit more intuitive, but the scaling was in my eyes to steep, so if you are a couple of levels to high or low you miss to easily or get hit too often.Good lord, AC 20 + level is "good"? Okay, see, this is where I want to flip out and stab D&D in the face.
I want to play D&D to be a big guy in full plate with a shield, or a nimble guy in leather, or maybe a kung fu guy who dodges because he's all zen and stuff.
I don't play D&D because I want to buy items that give me +1 deflection, +1 natural armor, +1 enhancement armor, +1 enhancement shield, +1 luck, and boosts to my Dex. That stuff really REALLY bores me, especially as a GM because a ruleset that requires those items just causes me to spend pointless time picking out gear of appropriate value in order for an enemy to be a decent challenge.
I definitely don't want to have to include giants, nets, and NPCs with dispel magic in my 'fantasy spy mission' adventure, simply because one PC is not threatened by mortals. I was running 4e before, and got fed up with the way it let players stack tons of debuff effects on prominent enemies, so we switched to PF, and now it's the math that's beating me up.
I really think I'd rather just convert to a system where my intuition about how challenging something should be in a 'Hollywood physics' world is matched by the system. John McClane survives Die Hard because he's a scrappy hero, not because he was kitted up like a magic Christmas tree.
. . .
I may be somewhat emotional as I'm writing this.
Anyway, my way of handling this in 3e/3.5 was to either limit the amount of books or just mention that I didn't want over-the-top characters in one direction or the other. It's an easier way of handling complex systems like 3.x or Pathfinder instead of working with the math. I think it's important to remember it's a pen-and-paper rpg, not a crpg. You can actually come to an agreement with your players about what kind of game you are running.
... My current 4e character is a Wizard. He could potentially have lots of status effect powers, but I mostly went with high damage powers instead. Nothing is as boring as an encounter that just goes on and on because the bad guys have been neutralized and the PCs are all low-damage survivalists.
Anyway, my preferences are quite similar to yours, I don't want to be bogged down with game mechanics when I am running a game. I want to focus on creating fun adventures and combats.
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