I don't know that my advice would help you much here. One of my biggest criticisms of 5E (aside from healing) is that the stats are too similar, and it's hard to figure out which one applies in any given situation - things like Perception keying off of Wisdom, while Investigation goes from Intelligence, so whether a given check is one or the other could be the difference between rolling at +20 and rolling at -1.
I also feel like a lot of stats are too easy to ignore, like how a Dex-based fighter can swing a scimitar and completely ignore their Strength score. It would make more sense, to me, if all melee attacks were governed by Strength. And for the same reason, if spell save DCs were all based on Int or Charisma or whatever, then that would also solve a lot of problems.
As a general guideline for game design, it's better to avoid anything that takes an average of two stats, because it makes it too hard to improve that thing later on. If your Swim is equal to the average of your Strength and Endurance, then it will be a pain to improve your Swim skill later on, because you could improve your Strength by +1 and your Swim might not change at all.
One way around that is to make your bonus equal to the sum of two stats, so your bonus to Swim would equal the sum of your Strength and Endurance, and improving either one would automatically improve the skill by the same amount. The limitation there is that your bonus to the skill check will always be larger than the bonus to either constituent stat check (e.g. it is way easier to hit a DC 17 on a Swim check than on a Strength check or Endurance check), but that's not an issue if everything you roll is a skill check and there aren't any checks where you only add a single stat.