General Annoyance Across Games:
- The care and treatment of Epona. She has the saddle on all the time. She never gets a stall /stable to call home - she's always tied up or running free in dangerous country. She always comes when you call. She never needs to be fed, watered, shod or treated for colic. You can plant arrows in her head and she doesn't care. It's unrealistic! (Okay, so I sort of have a beef with how horses are handled in most games... if it was made realistic, most players wouldn't have fun). In that vein, where do Loftwings roost at night? Why do they never poop? Maybe it would have been gross, but a poo-poo bombadier game might have been fun! Is it too much to ask for a little realistic biology in a videogame?
- Hyrule / Termina / The Sky et. all are TINY and LARGELY DESERTED. This is where an old 8-bit title beats out the fancy 3Ds for me: "Adventure of Link" had lots of towns... with people! Sure, they were the same people/same character-types and all two-dimensional, but towns that were full of people existed! All other games have Hyrule as a ghost-town kingdom. They don't need a royal family... with the population "density" they barely need a mayor!
(Alright, so I've played Team ICO's games, but they actually have an excuse for the sparseness... deserted castle ruins where the progatonist was offered as a starvation-sacrifice, a cursed land the protagonist isn't even supposed to be in... Hyrule's supposed to be a living kingdom, durnit!)
Specific Game Annoyances:
The Spinner in Twilight Princess. Maybe if it ran longer, but as it is, it's a top that peters out after a few seconds unless you find a specific kind of wall. It's annoying and I think it is the stupidest tool/weapon in the series. Most people list the Dominion Rod as that, but, I honestly enjoyed that more than I did the Spinner.
The cloning in Minish Cap. I ranted about it in a Minish Cap thread. It seems not to bother people, but I *HATE* the puzzles that require clowning. I hate the clones. They're too fragile and generally derpy.
Fandom Annoyances:
People hating on Link's companions. Jokes? Okay, I make those, too. I make lots of Navi jokes ("I want to put Navi in a bottle!" and the like), but when someone's dislike of Navi, or Fi, or any of the others borederlines into an actual hatred with enless gorey "fan arts" and fan fictions about Link killing his companions I kind of want to back away and say "Ookay, you do know it's just a game, right?"
The personification of Dark Link. If you're going by Four Swords manga, it's okay, because it's "canon" there, but otherwise (such as in Ocarina of Time) I have a bit of a squick over Dark being portrayed as an actual, fully-fledged person. It doesn't matter if you pair him with Link, or with Zelda or have him alone but with a personality, I just don't like seeing him as an actual "him" enough to know love or lust or remorse or anything - I see him as a spell or as an "anthropomorphic representation of the evil that hides in Link's heart." If you personify him, it's okay, I just tend to avoid fanwork with that kind of bent because it's a personal annoyance / difference of character interpretation of mine.