These two, yes.

Add Gaia's Navel from Chrono Cross to the list for me. Everytime I play the game, I loath this part because it feels like such a waste of time. Basically you just run around beating enemies until the boss finally decides to show itself. It isn't hard or tedious in any way...it just kills my momentum.

And I have one for Chrono Trigger as well. The Lost Sanctum content in the DS port was a huge pain in the ass. You can get some good gear, better than what was previously the best...but the entire sequence was a chore. I can appreciate what they were trying to do (give a glimps into the Dinopolis timeline referenced in Cross), but they went about it all wrong. It was just a series of tedious fetch quests that required a ton of back tracking, that added nothing to the plot overall.

Thunderblight Ganon in BOTW. A sharp and very frustrating difficulty spike.

Final boss fight in Uncharted Drake's Fortune. Just poorly designed and neither fun nor satisfying.

The Jiggy behind the ship's propellers in Banjo Kazooie. The engine room is a frustrating death trap to begin with, having to do it under time pressure is torture.

That boss is flat out unfair from what I remember. Also just sucks in general. 

Yeah I definitely felt he was unfair; his dash attack has inconsistent timing, sometimes striking right after a dash and sometimes waiting half a second which makes getting the dodge timing reliably right almost impossible. A horrible blight (heh) on an otherwise amazing game.

I distinctly remember is being variable, that was the only reason I had so much trouble.

I prefer the boss design of games like Ocarina or Twilight Princess personally, but aside from Thunderblight I still enjoyed BOTW's bosses.

The patterns may have been simple but I still found them satisfying to execute and their designs were badass.

He was the only real threat in the base game boss wise.  Really fun fight, especially if you have flurry rush or shield parry mastered.  The only way I see him being "unfair" is if he was one of the first blights you face, since bosses don't scale with the player and you would still be newer to the controls.  For comparison, he was my 3rd blight so I had the Master Sword by then and had gotten really good at flurry rush.

It was the first blight I did. 

Ouch, then yeah I can see where you might have had problems lol.