So long as the baseline game has set Ability/Skill combos, then there will not be sustantative changes to the skill system. Because for instance... Nature is an Intelligence check for knowing lore, which does not apply to the Wisdom check needed/wanted in the system for both Animal Handling and Medicine... so the game wants both skills in it. Likewise the need for both Athletics and Acrobatics so long as one triggers off Strength and the other off Dexterity.
Now that being said... if WotC decided to bring the variant rules of 'Alternative Ability Scores for Skills' forward and made baseline... then yes, you in theory could make changes to the skill system. You could get rid of Acrobatics and instead just ask for STR (Athletics) checks for climbing and swimming or DEX (Athletics) checks for balance and tumbling. Likewise the four "lore skills" (Arcana, History, Nature & Religion) could all be used with other ability scores for their different functions-- WIS (Nature) for animal handling for instance. Or consolidate Deception and Sleight of Hand and make the former CHA (Deception) and the latter DEX (Deception).
However, that being said... I do not believe WotC will in fact do any of that, because in order to maintain backwards compatibility there would be many places in all the older adventure books where they would be calling for checks that might no longer exist if they consolidated or changed the skill system. And in truth... the skill system is such an easy place to houserule... any table that WANTS a different system can just make one for themselves. Heck, I don't believe I've ever used the standard 5E skill system any time I've run the game (other than the online pandemic game I ran just because D&D Beyond won't let you futz with the skill list enough yet and I wanted things easy for my players.)
But there's absolutely no reason why any DM shouldn't curate their skill list for the individual campaign they are running depending on the focus of the game. Like in my ancient Greek Theros game... I have added Warfare and Nautics to my skill list because war and sailing are two very important aspects of the campaign and I wanted more granularity. And because I don't like using the 5E Tool system, I add Mechanics as a skill that takes the place of Thieves' Tools-- and use DEX (Mechanics) to open locks and disable traps, while INT (Mechanics) is for all engineering questions and information.
Now that being said... if WotC decided to bring the variant rules of 'Alternative Ability Scores for Skills' forward and made baseline... then yes, you in theory could make changes to the skill system. You could get rid of Acrobatics and instead just ask for STR (Athletics) checks for climbing and swimming or DEX (Athletics) checks for balance and tumbling. Likewise the four "lore skills" (Arcana, History, Nature & Religion) could all be used with other ability scores for their different functions-- WIS (Nature) for animal handling for instance. Or consolidate Deception and Sleight of Hand and make the former CHA (Deception) and the latter DEX (Deception).
However, that being said... I do not believe WotC will in fact do any of that, because in order to maintain backwards compatibility there would be many places in all the older adventure books where they would be calling for checks that might no longer exist if they consolidated or changed the skill system. And in truth... the skill system is such an easy place to houserule... any table that WANTS a different system can just make one for themselves. Heck, I don't believe I've ever used the standard 5E skill system any time I've run the game (other than the online pandemic game I ran just because D&D Beyond won't let you futz with the skill list enough yet and I wanted things easy for my players.)
But there's absolutely no reason why any DM shouldn't curate their skill list for the individual campaign they are running depending on the focus of the game. Like in my ancient Greek Theros game... I have added Warfare and Nautics to my skill list because war and sailing are two very important aspects of the campaign and I wanted more granularity. And because I don't like using the 5E Tool system, I add Mechanics as a skill that takes the place of Thieves' Tools-- and use DEX (Mechanics) to open locks and disable traps, while INT (Mechanics) is for all engineering questions and information.