(1) Time sinks and unnecessary tasks spent making NPCs more detailed than they need to be.
Theres nothing unnecesary about having a thoroughly detailed world. A campaign world doesnt revolve around the characters and cease to exist when they exist stage left. It should keep going and evolving as people respond to developments in the world.
Having a thoroughly detailed world makes that better.
(2) Illogical NPC classes in the game-world which lead inevitably to butt-kicking turnip farmers because of the idiosyncracies of levels. I can't see how this isn't a versimilitude problem while an absence of NPC classes is.
This fallacy of butt kicking commoners is something you've brought up over and over again and its simply a ridiculous strawman.
Most of those NPC classes gain +1 ATT bonus every 3 or 4 levels, so even metropolis size cities should only have 4 or 5 10th level NPC's. Who will certainly be gaurds and wizardly adepts, not farmers and still only have a +3 ATT.
So do i think theres a problem with the fact the occasional farmer who uses tools (tools which historically doubled as militia weapons) every day for a decade or two is good enough at swinging it to get a +1? No I am not.
Nor am I terribly concerned that a tough old laborer might have a whole 9 or 10 HP. IF he's managed 3rd or fourth level. As a D6 HP with no con bonus only nets you 3 HP a level.
(3) It throws class/level into every discussion of beings in the gameworld when it's a very clumsy attempt at obsessively categorizing the universe. Square pegs, round holes.
No, its square pegs with square holes in a very tidy way of categorizing the universe.
(4) Extraneous math which uses a process as a screen. It's fake versimilitude - you're following a process, so it feels like you're doing something, when in fact the math just obscures the final intent..
Its absolute true verisimilitude, everything works the same way for everyone. Thats the right way to do things.
Your assertion assumes theres any final intent other creating a believable logical NPC. Thats another strawman. The intent has nothing to do with the PC's which seems to be your assertion.
You can rattle it off because you've had practice and experience in the system. I should note that, like any new DM, it was not so easy at first. As with anything else, it takes practice. I'm also not a fan of barriers to new DMs. New DMs shouldn't have to go through a long process to figure out how good the village blacksmith is at making horseshoes.
I dont give a damn HOW NEW you are as a DM. If you have a hard time managing Level+3 max skill ranks you have no business whatsoever behind the screen. Put it down and hand it over to someone else who can manage it.