Yeah, I actually don't remember hating that part of the game. I mean, I didn't LIKE it, but I was the kind of person that spent 3 hours just sailing and unlocking the map for fun so I guess I'm really not a good gauge of what is and what is not a waste of time. If I like a game enough, I don't mind some grindy nonsense. 

Ironically, I don't like Ocarina of Time but actually do like the Water Temple. I know why people hate it but I dunno, I never really felt it was all that bad or hard. No different for me than any other puzzle dungeon in the history of the franchise. 

Double-ironically, there are few areas in games I hate more than the forced steal section Yuga Tribe hideout infiltration. Breath of the Wild is one of my favourite games but that's like the one part of it where I'm like 'fuck this shit' and just brute force my way through till it's done. 

In fact, I hate EVERY forced stealth section in games that otherwise are exclusively action or adventure. MJ/Miles morales segments in Spider-Man are good examples. I know why developers do this sort of shit - they like to diversify their game - but I don't think it ever works without massive caveats. either the player's headspace isn't in the right place and they just wanna punch things, or the mechanics aren't nearly deep or well-designed enough to work without frustration. Again, I don't mind the idea behind diversifying, but I think it's best to either incorporate that sort of shit into the game throughout in a way that benefits the player and gives them options, or leave these segments out entirely. Just switching to a wholly different gameplay mechanic for segmented parts and completely ending the mission/level if you get caught is bad design and literally nobody ever likes it. 

On a related note, I hate boss battles or sections that have completely unique mechanics or otherwise completely retract all the skills you've learned up to this point. ESPECIALLY end bosses where you don't fight with your own accumulated skills and items. I can't think of any examples right now because I'm recovering from being sick, but there are too many instances where I'm playing a game, unlocking skills, levelling up, refining my abilities, and getting the best weapons and equipment...only to be told I have to play a section or boss with shit the game gives me. Like, no you're not fighting with your honed and stylish skill, you're doing a giant mech fight now. Or FFXV with chapter I think 13 where you just have the 'hold to drain enemy health' button. 

Do what Grand Theft auto or Red Dead Redemption do. If you're gonna incorporate different gameplay elements into your game, then do so and commit to it. Don't make a game 98% one gameplay style then add one mission where you're doing something else just for token variety. 

Uncharted 3 - the ship yard - I don't know where to go, it kills the pacing, does not look appealing, is way to long

Batmobile sections in Arkham Knight. Soooo tedious and repetitive.

I can think of a number of these

TLOZ OoT - Popular pick, but the Water temple. Its not hard, its just a drag, and drags for too long. Which in turn makes it unenjoyable for me.
TLOZ BOTW - Amongst other things, the 4 divine beast dungeons are boring, bland and I'd argue badly designed/conceptualized.
DKC 2 - Cant stand the "thorny vine" levels, but the music is awesome.
Dark Souls 3 - The whole Profaned Capital location. I dont know if I "hate it" but it feels "Underdesigned" or something. Plus theres those Monstrosities of Sin.
Crash Bandicoot - High Road. No need to explain why.
Suikoden III - Thomas's story chapter is very boring
Suikoden V - The entire first act of the game. Its VERY slow, it takes like 4-5hrs of game time for the game to finally open up
Final Fantasy XII - The anticlimatic final dungeon of the game is... anticlimatic.
Chrono Trigger - Not gonna spoil which one, but one of the endings is not as good as the other 11 endings.
DQXI - The vast majority of Act 3 and the fact that it undermines/erases the cathartic plot moments of Act 2.

The escort mission in Zelda Twilight Princess

The Whitney battle in Pokémon Gold/Silver

Some vehicle missions in Jak 3

Atlantica in Kingdom Hearts II

Remix 8 in Rhythm Heaven (NDS)

Nightmare Frontier in Bloodborne

Blitzball in Final Fantasy X

The stupid and/or oversexualized characters in Xenoblade Chronicles 2

Speaking of Uncharted 3, slowly limping in the desert killed the pacing as well.

It's "Water Level: The Thread".  Every time someone mentions a water level, then you have to take a drink.

My most notable water level goes to Sonic the Hedgehog 1.  For decades I thought it was a reasonably good game, but I never made it past the water level.  Then a few years ago I made it past the water level and beat the whole game a few days later.  That is when I realized how great a game it really is.  It's solidly in my top 50 greatest games.  If it weren't for the water level, it might be in my top 10.

I co-sign this

Hate is hyperbole for most of this. I can't really think of any sections I full on hate. But there are certainly plenty that I dislike or barely like.

Final Section of the Ripto Fight: Spyro 2
Corona Mountain Boat Ride - Super Mario Sunshine
Rotation Puzzle - Star Wars KOTOR II
Chapter 2-3: Super Paper Mario
Tilt Sections - Super Mario Galaxy
Water Temple - The Legend of Zelda: Ocarina of Time 3D (I still don't mind the water temple, thanks to the streamlining in the 3D remake. But yeah, it's not too enjoyable).
Shipyard: Uncharted 3
All Searching for Clues from NPC sections - Persona 4 Golden
Tilt Sections - The Legend of Zelda: Breath of the Wild
Mary Jane sections - Marvel's Spider-Man