Okay, I guess we can do this instead.
None of those are particularly contentious and how to address those issues in a D&D context has spawned multiple long threads.
I held forth a broad category of fixes for D&D 3.X's skill system, that category being fixes that did not overhaul the system on a fundamental level. Claiming that D&D 3.X's skill system requires fixes is not actually a counterargument. It is part of my premise. Normally I'd assume you were making the claim that the category of fixes I was endorsing is insufficient for these issues, but then you listed "you would have to fix the Profession skill" as a counterargument to my claim that "you would have to fix the Profession skill," so I'm pretty confident that you've just failed to read and comprehend my post altogether.
The Sage Problem. Shit is supposed to happen when you have 10 ranks of Bear Lore, but you have to be 7th level to do that.
The highest Knowledge DC given in the rules is 30, both in being the highest DC explicitly given and in being the difficulty for knowing the vulnerabilities of a 20 HD creature. Assuming we are doing the obviously correct thing and having everything that references HD instead reference CR, because that is the thing that
actually maps to level, there's almost nothing that a character with +20 to a Knowledge check doesn't know and understand. You can get to +11 at level 1 if you have an apprentice, and up to +13 if you get a +2 circumstance bonus from having a library at your disposal. At this point, a sage can hit DC 30 by taking 20, which means the sage might need anywhere from two minutes to twenty man-hours in their library to come up with an answer to almost any question, depending on how long making a single roll is supposed to take.
With just two levels in a d6 hit die, 1/2 BAB NPC class, he can get himself up to +15 and hit DC 25 on a take 10, while sporting an average of 10.5 HP (assuming he is of average Constitution and is no more than 34 years old ) and a +2 attack bonus with whatever simple weapon he arms himself with. It's kind of weird that this guy stacks up about on par with an orc and if that really bothers you, you can create an NPC class with +0 BAB all the way to level 20 and no hit die advancement at all, but it's probably not a big deal because this guy already knows the secrets of astral devas and neothelids while being a combat threat of about CR 1/2 who compares unfavorably to a black bear. You can also use the 0 BAB class if it is for some reason advantageous to have DC 35+ knowledge checks actually do something definite and you want a sage to reach that level without stacking up hit points and attack bonuses. Either way, the "sage problem" is in 3.X is mainly an artifact of orcs being so close to frail old men in battle capability that an extra seven hit points and +2 to attacks makes the frail old man nearly as dangerous, and also I guess a serious misunderstanding of how high level a specialist build has to be in order to hit the highest DCs for knowledge checks given in the book.
The bonuses problem. The difference between a large rank bonus and no rank bonus is pretty big. At 7th level it's half the fucking RNG by itself. But the difference between a level appropriate rank bonus and a slightly lower level rank bonus is trivial. Being higher level as a specialist is only worth +1 per level, which is substantially smaller than picking up any other bonus at all, and is something you don't even notice on slightly more than 9 out of 10 opposed tests.
Partly this is an issue of lack of discipline in skill bonus sizes and types, making it easy to stack them to the heavens, and that is an issue with having spells, feats, and items that are heedless of the math on skills. But outside of builds that break +50 skill bonuses at level 10, this is mostly just not an issue. It is a good thing that a small child's size bonus gives them a noticeable edge over a fire giant with zero ranks in Spot despite the vast gulf between their combat ability, and while it
does make the math slightly more complicated and you could streamline it if you really wanted to, it is not a big deal that a bunch of your bonuses are derived from things that are level-gated rather than being derived directly from your level. The issue exists because it is too easy to stack a racial bonus, two feats, and a class feature into a +10 bonus, and because there exist items that just give a +10 bonus outright, and while you could imagine these things being written in such a way that they were level gated, they weren't.
The hidden child problem. Sneaky kids can't hide from stupid giants because Fire Giants have 18 ranks in fucking Spot.
Maybe we should reconsider the wisdom of giving our fire giants three times as many ranks in Spot as they get in Intimidate.
The non-functional subsystems. It's commonly acknowledged that Diplomancy, Stealth, and Profession don't work at all. Not to put too fine a point on it, but those are real important subsystems for your game to return "divide by fruitbat error" on.
I pointed this out earlier, but for the sake of thoroughness: Yes, that is a thing that I said would have to be fixed. Profession, specifically, was the example I gave of a skill that would have to be fixed.
The failure rate problem. The comically high failure rate of skills rolled on a d20 is acceptable - even cute - when dealing with 1st level fuckup adventurers. The fact that it pretty much stays like that even as the rest of the signifiers of the character change to depict them as seasoned badasses is not acceptable. The wizard can shoot lightning bolts out of his hand and the rogue still has a pretty significant chance of falling out of a tree.
This is a fantastic argument for reclassifying a tree from DC 15 to DC 10, under the grounds that 1) it absolutely fits the description of "[a] surface with ledges to hold on to and stand on" and 2) an average person can climb a tree in non-threatening circumstances, so being able to get up a tree by taking 10 should be possible for any random peasant, and a level 5 Rogue with max ranks and a stray +1 from anywhere else at all (including ability bonuses) will have no chance of failure. More broadly, it's a good argument for spot-fixing skills so that things an ordinary person can do when not under pressure are DC 10, and scale upward from there.
Suffice to say I am taking it as given that a character could hypothetically know a lot about bears or be good at painting without also being a badass - which right away implies a skill system that honestly doesn't look a damn thing like 3rd edition's (or 4th or 5th edition's, for that matter).
NPC class with +0 BAB and which doesn't receive hit dice but which still gets skill points. This is a slightly janky class, but it allows for characters who are very good at painting without ever getting even slightly stronger in combat, without rewriting a single word of the skill system. You would want to rewrite some of the words of the skill system anyway, but it's totally unnecessary to the challenge you issued.
The issue is that you should still expect to be a level 6 Rogue if you want to become an Inn Keeper via the Puss in Boots route of simply declaring it so.
That's weird. I would've expected the issue to be something we disagreed about.