Needing to read the encyclopedia just to understand the story
I think encyclopedia's in RPG's are great, but when you need to read them just to understand what the heck is going on in the story something has gone terribly wrong. Good writing should not require a PhD in the game's terminology. Final Fantasy XIII is a prime example of this and it made the storytelling a catastrophe.
Naming characters or places after food items
Look, naming your character after something edible might be cute once, but it gets old quickly. If you are a writer and you lack inspiration to the point that you use food items as names then it might be time for a long break. Using food is as stupid as using a safety pin as an enemy. Magical Starsign and Hyper Dimension Neptunia are good examples of this idiocy. Speaking of Neptunia, that whole game is so annoying it probably deserves a headline of its own.
Getting way overpowered for doing a lot of side-quests, turning the main quest into easy-mode
This might be a minor issue and it is something that happens in most games, but I really wish that more games used a scalable difficulty system for the main parts. In both Xenoblade Chronicles and X all I had to do was touch the bosses and they would explode because silly me took on a few side-quests too many and my party became godlike.
Taking the quantity over quality route to increase the game's length
I personally don't need every RPG to give me over a hundred hours of playtime, and if increased length comes at the cost of less quality content then I'd much rather take a short game. Xenoblade Chronicles X really hurt my feelings when it threw the lobster quest at me, which had you search for a hundred small red lobsters across the city. These could be seen from a distance so theoretically it should have been easy to fly around with your skell and pick them all up, but because of how the area loading system works you would not see any pop-up markers for many of these lobsters turning the quest into one of the most annoying "find the nail in the haystack" quests of all time. And the game already had an insane amount of content, so why the devs didn't cut that quest is beyond me.
And in that not-so-good game Hyper Dimension Neptunia they increased the amount of levels by taking the small amount of levels they had and copy-pasting them like crazy. Sometimes the very next area you got to was a carbon-copy of the previous one. To pour salt on the wound the levels weren't even good to begin with. Seriously, when creating a two-room dungeon is accomplished by taking the first room and reversing the enter/exit points to "create" a second room it's time to stop and re-evaluate our position. It did give me a laugh though, so that's something I guess. And I know I'm ripping this game to shreds in this post but it really pissed me off that much.
Stupidly long attack animations
Yeah, it's nice with really cool special attacks that blows up planets and whatnot, but the cool-factor disappears when you have to watch these attacks again and again because no one considered the option of making long attack animations skippable.
Finding collectibles that do not want to be found
Collectibles aren't bad, except when they are hard as hell to locate. Finding certain collectibles in Xenoblade Chronicles was a pain in the behind because the world was huge and directions non-existent. In X you had an excyclopedia but unfortunately "You can find it in Primordia!" is a really, really vague hint.
Trying to find NPC's or places
Yeah, another part of Xenoblade Chronicles that was a wee bit annoying. So you met an NPC, got a quest, finished that quest and are on your way back to the NPC. But you have forgotten where you met the NPC, and the game does not give you any directions so you have to waste time searching. It gets even better when there's a day/night-cycle and the NPC change position or disappears during certain hours. Fun!
The map/journal system of Baldur's Gate II isn't standard
Baldur's Gate II had a nice map with markers for locations (and I think NPCs as well) but the best part was that you could add your own markers and add your own notes to your journal! Why every RPG doesn't do this is beyond me.
