@Yaarel i havent followed this thread very closely. How do you handle the pairings of attributes and skills?
Skills are interesting to me in 5e as they strike me as one of the most modular components of 5e. Changing abilities has effects on various class abilities and can make modifying them difficult where as skills often can be changed with little to no impact on other rules in the game.
Skills are important in our games to adjudicate narrative scenarios. Many ideas to successfully overcome challenges never reach combat.
The abilities are important because they are aptitudes. Each is a cluster of skills that a character will tend to be good at generally, even if without training. I prefer to call them "aptitudes" and "aptitude scores", rather than "abilities". They are exactly an aptitude, whereas an ability can vaguely mean anything. To improve an aptitude while leveling is something like cross-training, getting better at a flexible cluster of skills generally, in a way that is more adaptable for new challenges.
Normally, we use aptitude checks, and players can choose to add whichever skill seems to make sense in the challenge. (The DM decides if a skill can apply. But the players are thoughtful and reasonable. There is rarely a disagreement between player and DM, unless there is a misunderstanding about the nature of the challenge, which clears up easily.
So it will be easy for us to use either four aptitudes, six aptitudes, or eight aptitudes. Whichever aptitude best applies to the challenge is the one used for the check. Players can choose whatever skill seems relevant and add its bonus to the check.
Of course, players prefer to choose a skill with a higher bonus. But this is the skill that the character is good at, and can use more resourcefully. So this tendency is working as intended. It deepens the flavor of the character, when a player describes how the skill applies. The only question is if the skill genuinely applies to the challenge. Again, the players tend to be fair and honest.
Tools are skills. Tools expand the list of possible skills. The skills proper tend to be a general theoretical knowledge. Tools tend to be a specialized applied knowledge. Compare the difference between Deception (Intelligence for fraud, Perception for replica, or Charisma for acting) versus the Disguise Kit. Where Deception proficiency can be used for a variety of applications generally, the Disguise Kit proficiency relates to anything and everything relevant to creating or using a Disguise Kit specifically. For example, one could use the Disguise Kit proficiency to mix chemicals to create a substance suitable for altering the features of the face convincingly, while the Deception skill could not be used to create this. Oppositely, one could use Deception to deceive a leader about some political affair, but could not use the Disguise Kit to do this.
Note, my character sheet organizes the skills proper into Physical skills, Social skills, Knowledge skills, Magic skills, and Tool skills. The Magic skills are Arcana, Nature, and Religion. Earlier Religion felt redundant because History (culture) and Arcana (spells, planes) are more useful and replace it. Meanwhile Survival is more useful and replaces Nature. For this reason, I have been rethinking these skills.
• Arcana ≈ Ethereal Plane, Feywild, Shadowfell, magical force, telekinesis, force constructs.
• Nature ≈ Elemental Planes, elements, plants, elemental magic, alchemy, chemistry, physics, animism, wilderness, cosmos
• Religion ≈ Astral Plane, Celestial/Fiend, thoughts, dreams, symbols, languages, worldviews, meaning
Nature applies to Plant as a kind of element, but not to animals. Animal Handling normally applies to nonmagical challenges, but also applies to various magical challenges. For example, it can recognize that an animal is actually a wildshaped Druid and facilitate "eye-of-newt"-style potions that transfer creature properties.
These three plus one skills turn out to be a great way to divide up magic, thematically. Each skill is useful. Nature turns out to be highly useful. Even Religion becomes necessary for many planar campaigns.
It seems to me, 5e somewhat stumbled into the concept of tool proficiencies accidentally. But because of its specialization and crafting applications, flexibility and verisimilitude, tools make 5e the best edition for skills so far.