** All experience goes back down to zero when you lose all your lives and get a Game Over. 20 EXP away from a level up? Too bad, it's all a waste, should have gone to an easier area to grind that last bit. And those big EXP pick-ups you grabbed during this time? Oh, they're not coming back. And this isn't even taking into consideration the large number of enemies who steal EXP whenever they hit you. They can't drain levels from you, but if you've collected 200 EXP and are 100 away from a level, getting hit enough will force you down to 0/300 EXP to the next level. Basically, in order to level up efficiently, you have to make sure you're not anywhere near EXP drainers (and they're annoyingly common).
** After getting a Game Over, any extra lives you've picked up (and there aren't too many of them) are LostForever. It also sets you back to Zelda's palace at the very start of the game, [[AntiFrustrationFeature except once you get to the last dungeon]].
* ''[[VideoGame/TheLegendOfZeldaOracleGames Oracle Of Ages]]'' added a [[SarcasmMode wonderful mechanic]] for the Mermaid Suit. You have to ''constantly tap the D-Pad'' in the direction you want to swim in, not hold the D-Pad as usual. This makes the sixth and seventh level bosses extremely annoying, thanks to both fights being fought underwater (the sixth boss is both under and above water).
** Made even worse in their Virtual Console release on the 3DS. You either had to double tap the circle pad (which is as inefficient and potentially inaccurate as it sounds) or, on an original 3DS at least, an incredibly stiff D-Pad.
* Having to pause and go to the equipment screen to change between normal shoes and iron boots over and over and over in ''VideoGame/TheLegendOfZeldaOcarinaOfTime'''s Water Temple, where you need to walk on the bottom in some places and float in others to complete it. (Thankfully, the remake and next games have the Iron Boots as an item you can equip to one button for easy switching.) Made worse by the fact that it takes ages to switch to the pause screen, as every time the player presses the Start button, the game slowly generates a screenshot of the game in order to use it as the background for the pause screen, not showing this one until the process is finished.
* When you travel back to the First Day in ''VideoGame/TheLegendOfZeldaMajorasMask'', you lose certain sidequest items such as Deku Deeds or the event items involving the Anju and Kafei sidequest. Considering how much time it takes to get each portion back if you reset time and save, it's highly annoying; especially as Anju and Kafei's sidequest needs to be done twice to get 100% for the game.
* Kinstones in ''VideoGame/TheLegendOfZeldaTheMinishCap'', for wasting one of the GBA's precious four buttons on a seldom-used function. And the people you fuse Kinstones with keep changing. You could attempt to fuse Kinstones with somebody, discover you don't have the right type, and come back later when you do to discover that that particular fusion has moved to someone else. It's particularly bad when there are certain fusions that will always be from a specific NPC, but they won't always be willing to fuse Kinstones with you. Also, some possible Kinstone fusions will be LostForever if you don't fuse them at the time the game wants you to fuse them. It's especially annoying when at one point in the game, Tingle will fuse Kinstones with you, but come back later in the postgame with only one Kinstone left to fuse and he suddenly won't want to fuse with you.
* ''[[VideoGame/TheLegendOfZeldaTheWindWaker Wind Waker's]]'' sailing deserves special mention here; while it's essentially the same mechanic as Epona the horse, at least Hyrule Field has more visual diversity. Epona also didn't require you to play a song every time you wanted to change directions for max speed, and the Great Sea is much larger than Hyrule Field. Of course, a BrokenBase has developed around this mechanic, as about as many fans who hated the mechanic also loved it. Slightly changed in the UpdatedRerelease with the addition of a "Fast Sail" that doubles your speed and eliminates the need to manually change the direction of the wind; of course, the issue of whether it's needed or it ruins the experience of the game leads back to the same argument.
* From ''VideoGame/TheLegendOfZeldaTwilightPrincess'':
** You found a silver rupee! That's worth a whopping 200 rupees... but your wallet is full, so let's put it back for now. Some may find it better than the alternative used in previous games where any found rupee would be ''erased'' if you tried collecting it with a full wallet, but they may think otherwise while searching for the last "unopened" chest in a dungeon.
** There's also the annoyance of the game having to give you a description of higher valued rupees the first time each time you start up the game, even if you found them on the ground.
** The mechanic of being only able to call your horse at certain locations. While the grass needed to call it are stragetically set, it is annoying to have to walk back to a certain location since it's the closest place where the grass is located. Fortunately, the horse is barely needed after you advance in the game. This mechanic is made ''worse'' by when, very late in the game, you obtain an item that replaces the need for finding the grass and allows you to call the horse wherever you are, as long as it isn't inside a dungeon. And this item is given to you at a point when you have access to teleportation practically all over the world map, making it much less useful than it would have been earlier.
* Having to return to the central temple in ''VideoGame/TheLegendOfZeldaPhantomHourglass'', and repeating the same levels after each new item is found, in a timed [[UnexpectedGameplayChange forced-stealth section]] with invincible baddies gets old ''real'' fast. Thankfully, near the end, the player gains the ability to kill the Phantoms. [[MostWonderfulSound Hearing them die]] is worth ''all the trouble''.
** The train travel is this, mainly for three reasons: One, because of it, overworld travel is on rails, literally. Meaning that you can't freely roam and explore it. Two, if you happen to die (which is gonna be the case quite frequently, given the number of attacking monsters and evil trains in the open fields), you reset to the location you started. Three, somebody thought that it would be funny to complicate [[WarpWhistle the fairly simple teleport mechanics from the previous games]] down to the point where they are barely of any use anymore.
** Another despised aspect of Spirit Tracks are the Pirates. They are far more frequent than is reasonable, and are a severe threat. They lag the game, [[TheComputerIsACheatingBastard every shot they do after their first is 100% accurate]], and if you have a passenger, you'll have to do a very long and drawn out fight scene, where death and/or failure (requiring a restart of the already Scrappy EscortMission) is a very high possibility. Good news is, you can destroy the cannonballs they fire at you before they even make contact. Besides that, you can always slow the train down while carrying a passenger so that you lessen the risk of multitasking to both fend off the pirates and follow the signs.
** The Spirit Flute duets have a small hatedom due to the item's incredibly finicky and picky nature.
** Passenger missions as well, at least when you're forced to go through enemy-infested sections of railroad tracks. Your passenger will get increasingly annoyed with you each time the train gets hit, and fighting to keep the ship from being blown up by pirates apparently isn't a valid excuse for not ''blowing your whistle when a sign tells you to''...
** The Adventure Pouch is essentially a separate inventory where you can store up to 8 (with upgrades, up to 4 initially) items of your choosing. Except that said items are things that ''didn't even use up an inventory slot in previous games'', like Shields and Bottles. By far the most irritating, however, is the way ammo expansions work. Rather than simply getting a bigger quiver/seed satchel/bomb bag that replaces your old one, you have to ''buy an extra quiver/satchel/bag and have it use up an inventory slot'' just to be able to carry even 10 extra bombs/arrows/seeds. Said inventory slot could be used for a bottle or even a ''shield''. Oh, and in order to have a full life meter, you need to equip two 'life medals', meaning if you want it to look like you have OneHundredPercentCompletion, you'll ''need'' to use up two precious slots on those, effectively giving you only 6 slots to work with.
** There's also treasure. When you pick up a new type of treasure, you get the usual animation of Link holding it up and a text box announcing what it is, followed by your tally of that item going up by one. All well and good, except that this aspect resets ''every time you start up the game;'' anything you haven't picked up ''in the current game session'' triggers the time-consuming cutscene all over again because, evidently, [[ViewersAreGoldfish you are woefully incapable]] of remembering what a bird feather is between game sessions (or woefully incapable of looking it up on the inventory menu). Thankfully, this can be avoided by picking the item up with the beetle.
** This game also inexplicably did away with adjustable text speed, uses a ridiculously slow speed as the default, ''and'' has more text-exposition than any other Zelda game, so be prepared to sit through many lines of tedious text, often text you've been force-read dozens of times already, every time you buy anything or talk to anyone for any other reason. Plot-relevant text is even slower. Holding down the A button speeds it up a tiny bit, but not nearly enough to prevent boring an average-speed reader to death.
** The dash mechanic. Link's stamina can only be enhanced through temporary ([[RandomlyDrops and]] [[ItemCrafting expensive]]) potion effects, and given that Link walks so slowly otherwise, you'll find yourself constantly having to press the dash button just to get around. In addition, climbing walls and stuff now takes up stamina whereas in previous games you could take as long as you wanted to climb a wall so long as you didn't fall off. There are usually Stamina Fruits in both cases to mitigate the issue, but it still can easily trip up new players.
** While opinions on the motion controls vary, the lack of a left-handed option causes no small amount of agony to southpaws.
* ''VideoGame/TheLegendOfZeldaALinkBetweenWorlds'' has a frequent amount of AntiPoopSocking compared to the other games. "You've been playing for a while. Why don't you take a break?"