In non-4E versions of the game, it's bizarre how luck is vastly more important than skill. Even a 20th level thief rogue with expertise your roll on the d20 is still more important than your actual skill.
In 5E, it bugs me that damned near every class in the game is magic and every single class has at least one magic subclass.
In WotC versions of D&D, it bugs me that you heal, as if by magic, overnight. The default should be slower. It shouldn't be the Basic and AD&D 1/hp per day madness. But poof you're all better with a good night's sleep is silly.
I miss the various subsystems using different resolution mechanics. Doing everything as a d20 "unifies" the mechanics, but it makes everything the same and that feels boring. I miss 1d6 for some things, d100 for others, roll high d20 for some, roll low d20 for others, 2d6 for this, and 1d10 for that. Variety is the spice of life and all that.
And just to go full grognard, variable weapon damage still bothers me. Everything should be a d6.