Like Shilsen, I would expect that it's that way by design, for the most part.
Let's say you're a commoner who makes his living tilling the fields and driving the pigs to market in the spring. You want to catch the eye of that pretty girl in town. What's going to be your feat combination: Power Attack and Cleave, Skill Focus: Profession Farmer and Skill Focus: Diplomacy, or Spell Focus: Necromancy and Iron Will?
Approaching it from a different angle, let's say that you're designing the matron of a peasant family. She's in her late thirties and you've decided that she's third level. You want her to be able to spot a phony from a mile away, be an expert weaver (though she rarely has the opportunity to do anything that challenges her talents) and still remember how to use the longbow and spear that all members of her egalitarian community have to learn in their use. Negotiator, Skill Focus: craft weaving, and martial weapon proficiency: longbow seem to fit that role. That way, she's still third level and has very little combat ability, but with a decent wisdom, it will take a mid-level rogue to sneak a believable lie past her. Given a masterwork loom, she could weave masterwork clothes even though her Int is only 10. And since she's proficient in spear (the commoner's free simple weapon proficiency) and longbow, she's a believable former militia member.
On another angle, the skill focus feats allow a DM to create NPCs who are very good at doing something without being particularly high level. A 3rd level dwarven smith with max ranks, a 12 Int, Skill Focus: Craft Weaponsmith, masterwork tools, and an apprentice to use Aid Other will succeed on a DC 26 craft weaponsmith roll while taking ten as long as the weapon is made from stone or metal. But his combat ability is probably similar to a first level player character's. With the skill focus feat, he can be an exceptional weaponsmith without being particularly high level.
Then, think about the kind of people who go into adventuring. They're going to spend the rest of their lives killing an average of at least one sentient being per week and are likely to risk death a hundred times over. The ones who are actually going to succeed are going to have feats like Power Attack, Dodge, Spring Attack, etc. If they're wizards, they'll have Spell Focus: Evocation and Empower Spell (or spell focus: necromancy, etc).
Of course adventurers are going to have more combat feats and commoners are going to have feats that adventurers only very rarely take.
Aus_Snow said:
Actually Elder-Basilisk, I've wondered now and then whether that's a widespread phenomenon (NPC's having more of those types of feat than PC's). Other than to qualify for PrC's, of course.