For example, I find when I run there's a lot of athletics, acrobatics, survival, investigation, perception and persuasion checks.
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So at your table(s) what skill proficiencies get applied to a lot of meaningful checks?
I still have some open issues with overusing Perception.
I used to have too many Athletics and Persuasion, but eventually I realised the problem is not with the system. It is all our fault. We just assume that there HAS to be a check to resolve challenges, but that's not really what ability checks are for... their purpose is to resolve a DM's indecision i.e. when the DM doesn't want the responsibility to decide an outcome. Does the Barbarian break the door, does the Rogue find the trap, does the Wizard know the arcane symbol? The rules allow the DM to decide yes or no, or let the dice decide instead.
I used to call for a lot of Athletics checks but why? Why did I have to let the dice decide for every tree to be climbed, hole to be jumped or door to be forced? Having too frequent checks meant that Athletics had become a must-have or no-brainer at least for one PC in every party. But it also meant to have a LOT more failures than necessary, so I cut it short and let my players know I would not call so many Athletics checks anymore.
Persuasion had its own issue because it's used for contests (not always but still), and those make a lot more sense to leave it to the dice, since they are challenges between characters. It got used more often than Deception which in turn got used more than Intimidation, presumably because players prefer parleying nicely than aggressively (when they want to be aggressive, they rather attack). But I managed to balance the three of them better when I realized that Intimidation doesn't have to be called for only when the PCs want the targets to believe THEY are the threat, but also when ANYTHING ELSE is the threat. Meaning, use Intimidation whenever the purpose is to scare the target as in "if you don't do as I say, something bad will happen to you". It helped turning a lot of Persuasion checks into Intimidation.
That said, I still haven't managed to decrease the amount of Perception checks using similar ideas, mainly because of the checks against being surprised, they are still a lot.