I agree. There is a balance to be struck. If Athletics were 3 skills in 5e would that help or hinder martial characters?
This used to be the case back in Third Edition, but for rogues -- you had Hide and Move Silently as 'sneak' skills, which were opposed by Spot and Listen. You then had to have Search as a separate thing from Spot (because Spot was for opposing Hide, not for, say, looking for traps).
Then you divided Open Locks and Disable Device, because picking a lock and disabling a trap were different things in AD&D, and thus needed to stay different things.
The designers made up for it by giving rogues way more skill points, but that just caused different problems -- specifically the 'why do wizards get so few skill points compared to rogues' (wizards don't actually get that many fewer skill points, if you build your rogues with average Int, but nobody does that because they want All The Skill Points to get All The Skills).
Now, we have Stealth and Perception, and we have Thievery for all the thieving stuff. And in 5E, if you want to be a guy who knows how to pick locks but isn't all 'I know all the thieving stuff', you can be proficient with lockpicks but not with thieves' tools (it's sub-optimal, but you can choose it for Character Reasons if you like).
In fact, this is one of the strengths of the 5E skill system -- Performance technically already gives effective proficiency in all instruments, as long as those instruments are being used in a performance. You make a Charisma (Performance) check, and you get the proficiency bonus -- you don't get double the bonus because you're also proficient with the shawm. Being proficient in the shawm is helpful if you're not proficient in Performance, as well as for other checks you're not proficient with (like an Intelligence (Investigation) check to discover why your shawm is broken).
I like the idea of proficiency with rope use, and would allow a character to take (or learn, via Downtime) proficiency with rope as a tool to gain the proficiency bonus on tasks involving rope (so climbing a rope would grant the bonus, even if the character isn't proficient in Athletics).
It gets back, a bit, toward something that some players really liked about the old 3E Profession skill -- even if they seldom (or ever) used it in-game, it allowed them to say something about their character that was backed-up by a game mechanic; if I've got 10 ranks in Profession (Cook), then I'm a pretty danged good cook, way better than someone who just relies on 'natural ability'. I can't quite get to that level of a statement in 5E, but saying 'I'm proficient in Cook's utensils' says I'm a better cook than someone who didn't take that proficiency, and says something I feel is important about my character.
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Pauper