Okay, so the basic premise is this: 
NPC classes are horifically underpowered and completely unbalanced against eachother. I am here to fix the latter issue, not so much the former. I'm leaving warrior completely alone, in hopes of balancing the other NPC classes against them.

[Hider=Commoner]
Hit dice: d12

Class Skills: bluff, Climb, craft, forgery, gather information, handle animal, hide, jump, listen, move silently, profession, ride, search, sense motive, spot, survival, swim, use rope.

Skill points per level:
4 + Int modifier

Weapon and armor proficiency:
Commoners are proficient with all simple weapons, clothing and light armour.

BAB: 3/4 level.

Saves: Weak fortitude, reflex and will saves.

Ah, the commoner. This class was flat-out worthless. A commoner was so weak that at first level they would notoriously be killed in one round by a house cat. Well, the clothing and armour system in Aelsif already makes that unlikely, but a commoner shouldn't be losing fights with dogs or wolves, either. Putting aside that NPCs in Aelsif are very, VERY rarely first level, the commoner clearly needed some help. They are now they are a decent fighter but not as good as a warrior, and they have decent skills but not as good as an expert. They also won't be losing a fight with a house cat, to say the least.[/Hider]

[Hider=Aristocrat]
Hit dice: d4

Skill points per level: 6 + Int modifier

BAB: 1/level

Weapon and armour proficiency:
Aristocrats are proficient with all simple and martial as well as clothing, light and medium armour as well as shields (except tower shields).

I haven't changed anything else, why list it again?

Aristocrats are now extremely fragile and have inferior proficiencies, but have more skill points. This both weakens them to the same relative capability as a warrior with equal level and wealth, and gives them a role. They're fragile and can't handle injury, but they can have good attack, damage and AC and they have high skills, naturally suiting them for leadership roles. An aristocrat coming along with a group of NPCs is likely their leader, quite likely their diplomat and maybe even their translator, since they have the skill points to do all these things.
[/hider]

[hider=Expert]
Hit dice: d8

Other than a little bump to its hit dice, this class didn't need any help.
[/hider]


[hider=Adept]
Hit dice: d8

Weapon and armour proficiency:
Adepts are proficient with all simple weapons and clothing, but not armour or shields.

Familiar:
Works exactly as it used to, except at 1st level instead of 2nd.

Adepts now start off with only orisons. They gain 1st-level spells at 4th level, 2nd-level spells at 7th, 3rd-level spells at 10th, 4th-level spells at 13th, 5th-level spells at 16th and 6th-level spells at 19th.

Their 6th level spells are:
Heroes' Feast.
Banishment.
Wind walk.
Acid fog.
Chain Lightning.

More hit dice and familiar right away, less low-level magic and more high-level magic. Pretty straightforward.
[/hider]

Now, when you run into an NPC party, they actually work. Even if they're just a source of information, at least now they make sense. If they're allies on a side quest they're less of a burden and if they're a hostile encounter they may actually be at least somewhat of a threat (if not much of one) to a similarly-levelled player party.