tl;dr- The 6 ability scores are being forced to be used for things they were never intended for, Dexterity and Charisma should be split into two abilities each, Wisdom should be removed, and Awareness should become a new ability score.
Note: This post is inspired by this blog post by the Angry GM.
To open this bluntly, the 6 ability scores have never done a good job at mapping every characteristic a person can have, but they were at least serviceable in AD&D, because so many things used their own mechanics. For example, Thief skills had their own table with percent chances, a completely separate mechanic from the to-hit tables that would eventually become THAC0. But entering 3.0 and the d20 era, those skills had to go somewhere, and were assigned to Dexterity.
Notably, this even extends to things like the fanmade Pokemon Tabletop RPG, which uses the same 6 ability scores, despite much of it being completely irrelevant for Pokemon battling.
The 5 main problem areas I see:
Sorcerous Egos
The first thing I notice is the double meaning of Charisma. On the one hand, it represents personal magnetism and how likable you are. But at the same time, it also represents your ego and your force of personality. Not only are these not necessarily related, but in some cases, they can be inversely related. For example, in In Hell's Bright Shadow, Azvernathi Raul is described as having an ego and an off-putting personality. The former sounds like high Charisma, while the latter sounds like low Charisma.
This is especially notable because Sorcerers and Bards, the two classic Cha-casters, use these two different forms of Charisma.
Will Saves
This is related to the previous point, but I'm addressing it here because Will saves are traditionally assigned to Wisdom. I can sort of understand Wisdom to Will saves against illusions, but Will saves against charms and compulsions (i.e. the Irrepressible trait in PF 1e) sound more like Charisma, or at least the parts the sorcerer uses.
Perception
What does this have to do with common sense? The only reason they are is because there wasn't an ability score for awareness and perception in AD&D, so WotC just folded them into Wisdom instead of making a 7th ability score.
Thief Skills
These are interesting, because a lot of them fall under fine motor skills. But like with Perception, there wasn't really an ability score for that, so they got folded into Dexterity- the closest vague fit. But just like you can have an offputting ego or have plenty of common sense, but be unobservant, it's entirely possible to have a nimble tumbler who's all thumbs. Or on the other hand, you can have a character like Gepetto from Pinocchio. I don't think anyone expects him to be able to do gymnastics, but he still seems to be quite adept at clockmaking, which requires a lot of fine motor skills.
Dexterity Fighters
I'm not going to get into the debate about whether or not Dex to damage would make it an overpowered god stat, although I do point out that we're comfortable with casters being SAD. No, instead I'm going to take a look at what I suspect to be the origin of that archetype.
Swords don't actually require that much strength. Sure, an axe might, but levers and the slashing motion do most of the work with sword. Think about a steak knife. You don't need to be ripped to operate one successfully. (And on the other hand, archers do need to be ripped to handle things like the 180 lb draw strength of an English longbow) And that intuitive reasoning is why I think Dex builds all tend to use swords, instead of things like the equally finesseable club. The only non-slashing weapons I can think of that Dex builds use are the rapier and unarmed strike.
At least in AD&D, there were always notions of strength being physical strength and dexterity being agility. But because of the decentralized nature of game mechanics and the existence of minimum ability scores, Strength was first and foremost how good of a Fighter you were, while Dexterity was how good of a Thief you were. Thus, it made enough sense to have Strength apply to all melee weapons. But with the increased decoupling of class and ability score, your ability to finesse a weapon no longer had to be part of physical strength and could move over to Dexterity. Thus, Weapon Finesse was born. And as explained, the set of weapons that people typically use with finesse builds (swords) generally matches the set of weapons where dexterity makes at least as much strength as an attacking stat for anyone, much less just with Weapon Finesse.
My Suggestions
Split Presence off from both Wisdom and Charisma. It now represents your ego and force of personality, as separate from how likable you are. The three main uses for it are Sorcerers, Will saves, and Resonance.
Rename Wisdom to Awareness. It primarily governs Perception, but could also include things like common sense and Sense Motive.
Split Deftness off from Dexterity. It primarily represents your fine motor skills and things like Disable Device. However, there's enough wiggle room that I think you could reasonably include Weapon Finesse.
Rename Dexterity to Agility. It's larger level dexterity and is used for AC, Reflex saves, and Acrobatics.
And on a tangential note, assign different attack and damage stats depending on weapon group. Most things still use Strength for both, but Swords use Deftness for attack and damage, and Brawling weapons and Knives let you use the better of Strength and Deftness.
