Nobake: #1 gripe: first person perspectives in games that have it. Not limited to RPG's, I think there's about 4 games in all of history that I liked with a first person view.
My #2 gripe is with the games that just drop you in the world without any sort of direction or clue about about what to do or where to go. Maybe there's a backstory indicating the end goal of the quest (i.e. who the big boss is), but little to nothing on how to go about things in the immediate term. Mostly a problem in older western RPG's
#3 would probably be weight/encumbrance systems. Nothing like getting cut to 1/2 speed because you picked up a potion.
That's the main stuff. And I guess not really what the OP was going for, but there's plenty of silly idiosyncrasies littered across the RPG landscape.
Always fighting rats and insects (giant or not).
Fake choices, whether the ones where it repeats the question until you answer correctly or the ones where the outcome is the same regardless of your choice.
Having the power to kill the mightiest of beasts, but unable to kick down a door.
Low on HP? Go to an Inn! A single night's rest heals all wounds.
Your heroes are not subject to normal biological processes. They never need to bathe, use a toilet, or eat. Not that I want to see these in-game, but it's still kinda silly.
The dirty orc or nasty slime monster drops a piece of meat! Wait, you're not really gonna eat that are you?
If you want biological processes, play Realms of Arkania without investing in winter clothes :D