The Legend of Zelda
The Adventures of Link
The sequel tried to integrate more RPG elements into Zelda. Occasionally, while walking on the overworld, little black enemy silhouettes appear, frantically raving in blacklight. If you make contact with one of them, you get forced into a side-scrolling stage where you do nothing but fight enemies. Yeah, you might get a little experience, a little gold. But you're more likely to lose a ton of life.
A Link to the Past
Tossing Rupees into the Magic Fountain
I was going to say using the Magic Mirror to get places you want to go, especially trying to find the Lost Woods dungeon or using the duck. But this just takes forever and it's so asinine. First you gotta choose how many rupees to throw them in, wait for the fairy to s-l-o-w-l-y fade in and wish you good luck, scroll through dialogues, repeat the process. Can't the computer figure out I've got all my hearts and magic and I'm chucking in my life savings on purpose?
I blame the limited nature of the Game Boy on this, but still, it could have been programmed around. You have to frequently switch your main items around from arrows to bombs to Roc's feather to shovel to powder to hookshot. And couldn't they have made some of this innate? Like the Power Bracelet and Shield?
The Ocarina of Time
Nothing new here. Moving on.
Playing The Same Songs Over and Over
Due to the cyclical nature of Majora's Mask, you're going to end up doing the same things over and over again. The mini-quests havea lot of try-fail cycles. And to do some of these takes trial and error, spanning multiple days and pinpoint timing. That means a lot of waiting, a lot of mask switching, and a lot of ocarina songs.
And the only ones you really use are the "Song of Time" (plus its variations to slow down time or skip ahead) and the "Song of Soaring". Epona's useless since it's a hub world, and all the rest are quest-related. You're going to get pretty sick of selecting the ocarina, playing the song, playing it again because you messed it up, pausing to check the item screen to see how it's played, going back and playing it again, then warping, then unselecting the ocarina and reselecting whatever was there in the first place.
The Wind Waker
Interruptions in Sailing
It takes long enough to get from Point A to Point B as it is, even with warps. Between the barrel jumping and the tornadoes and attacks and futzing with the Wind Waker to get you in the right direction, I'm surprised you end up anywhere. They're probably meant to provide variety in the monotonous ocean, but they end up making the journey longer, so you end up avoiding them all, if you can help it. It's especially obnoxious during the Triforce fetch quests.
"You got a red (20) Rupee!"
Thanks, jackass. I know what a red rupee looks like. I just ran over it, or plucked it out of the treasure chest. I've only gotten a hundred of these before. I can see my wallet went from 0 to 20. I think it only does this once every time you turn on the console, but still, why you gotta be a hand-holder, Zelda?
Skyward Sword (a.k.a. Zelda: the anime)
For some reason, the constant rupee prompting got worse, not better, in the next iteration. And as a fun bonus, it also now applies to the sixteen treasures, twelve bugs, and all the ammunition. Combine that with lectures about falling off Skyloft (except in designated areas), the repeated dialogue from shopkeepers, and the game hand-holds you more than a pedophile at an amusement park.
But combine that with Fi, and you've got a recipe for turn-off. There is nothing redeemable about this character. They try and give him/her/it an emotional farewell at the end, but it's unearned. I felt more emotions when Navi flew out the Temple of Time window. Is there anything Fi won't remind you about? Christ, it even tells you when the batteries are low in your wiimote. Talk about ludonarrative dissonance. And everything's got a "percentage of chance" -- it's like a goddamn robot, but the game never explains this quirk of personality.