That no one is good at everything in reality, while in the game a know-nothing on a topic can get a great roll?It's not entirely clear what problem you are trying to fix.
So a big thing to understand about 5e is that it is a streamlined version of 3e/3.5/Pathfinder.
The more complexity you add, the closer to 3e you're going to wind up.
The precursor to the modern Proficiency Bonus method was introduced in 3.5e's "Unearthed Arcana" under the idea "Maximum Ranks, Limited Choices". Though at the time it still had "Cross Class Skills" at half-proficiency. Though arguably you could also say it came from the very next option (on page 81) of Level Based Skills, where you picked your proficiencies at level 1, then just used your Level as your Proficiency Bonus rather than having skill points at level+3 maximum.
Which, you are right, I forgot as a very crucial change in 5e (and a bit of a shame, if you ask me, as it really lowers the value of intelligence, maybe the solution lies into allowing intelligence to gain you some expertise, or half-expertise), but still minor compared to BA and Adv/Dis.In either case, you picked your skills at level 1 and they leveled up automatically with you, rather than getting different levels of skill point expenditures on different skills. The only ways to get more skills were Skill Granting Feats or increasing your Intelligence modifier.
4th Edition took that option from 3.5's Unearthed Arcana and ran with it, making it the default with players adding 1/2 their level to any skill in which they were proficient instead of your level or level+3 or full level.
5th Edition took -that- and added in Bounded Accuracy (since AC in 4e also went up with your level) to streamline it and make sure even a puny kobold had the chance to roll a Stealth Check that beats your Perception check. They did this by shrinking the proficiency bonus even further.
So... Yeah. It was absolutely an evolution of the 3e design. First streamlining point buying into a single choice made at level 1, then lowering the maximum skill check value, then lowering it even further for Bounded Accuracy.
Advantage was designed to support Bounded Accuracy while maintaining some measure of the old "I get +2 from being a catfolk, +1 from my magic cloak, +3 from my skill ranks, +2 from dex bonus, +4 because it's dark, and +12 because it's the last tuesday in June." modifier pyramids into a simple binary of benefit rather than a discussion of Bonus Typing and Stacking.
I think there is a simpler solution to this - gating things behind proficiencies.That no one is good at everything in reality, while in the game a know-nothing on a topic can get a great roll?

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.