Ok, this is confusing me... is your only problem with class based NPC design that combat ability rises with level? If so, then isn't that more of an issue with how the class was designed as opposed to the general system. I mena you could just as easily have a commoner class with little to no combat advancement. I guess I'm not seeing how this one issue that is being harped on by numerous people makes NPC's with classes a bad system as opposed to 3.x being an implementation of it they didn't like for their particular campaign world.
At which point you've got a Normal Man (to use the old name) who happens to have a high bonus in some skills. So what are they getting for their high level other than high skill in something, and why isn't it just simpler to give them the high skill without bothering about class/level?