One that annoyed me a lot was the Captain Toad last stage. A 50 level dungeon. A maze where you could never stand still. Avoiding everything for 50 levels and not getting caught by the thing chasing you. So very annoying. It's also so very hard. Much harder than the rest of the game. The thing that gets to me the most here is the stage is so different to the rest of the game. The rest of the game is very puzzle like. This stage is a super tough race for the most part. I never beat this stage. I have gotten half way though and when I failed, I just gave up. In my opinion this should never have been in the game because it's not what the game is about, a great puzzler.
Another one that exists is the Breath of the Wild, Master Sword Trials. Sure the beginner and middle trials are doable with some skill, but the expert trials are crazy hard. Many people ahve told me, they are harder than the last boss of the game even. Sure many people will say, a hard set of stages in a hard game is fine. But I disagree. BotW as a game is initally hard but with over time you get better at the game and it's not so hard anymore, and the game is about exploration first and everything else second. A side set of challenges this hard is just not fun and is very out of place within what the game is. No one like Zelda 2 - Adventure of Link because of the difficulty curve there, but they seem to be ok with the BotW expert trial which is even worse as it's a concrete wall of a difficulty spike. BotW is about time spent in the game and exploring to get the 100% completion. This Expert Master Sword Trial goes against what the game is about and that's why I don't like it.
I didn't know Galaxy 2 did this.
Galaxy 1 had this with the Melty Molten Galaxy stage. The Daredevil version of this stage gives you only 1 health. Get hit by anything and boom, stage over and you have to try again. It's quite hard actually. That purple comet (one health only) version of the stage is a lot harder than the rest of the game. Took me quite a few tries to get it done.
However the Galaxy 2 Grandmaster Galaxy (Perfect Run version) which is the one health only version of the stage is a real nightmare. Apart from one health only the stage removes all checkpoints as well. Which makes it even harder as it's quite a long stage. The best I've done on it is I got right to the end once and lost to the Hammer Bros at the end. You have to beat 3 of them at the end to beat the stage.