You couldn't save Solaire after a certain point. And it was pretty unintuitive to know how and when to save him. So, even Dark Souls commited that sin. Also, to unlock a certain covenant, you had to do some weird stuff. And that as well, if I recall correctly, wasn't reversable later on in the playthrough. But I'm not that sure about the covenant.
I hate that. I really do. You have games, where you're not able to think outside of the box. Imagine that in a CoD. My mind would explode. So it becomes a given. OK, let's narrow it down to RPGs. Normally, that is the point of the genre - to tailor a bit the story here and there. So RPGs get a pass from me.
Now, you have Dark Souls. Is it an RPG? Puh... Now, I love it. For me, Dark Souls is the third coming after Terranigma and Silent Hill 2, but... is it really an RPG? Is Final Fantasy an RPG? It has elements. Final Fantasy has an mostly accepted combat and character developement system. But story-wise? It's linear.
It's like food. Those games, Dark Souls and Final Fantasy, are dishes you order in a restaurant. It's premade, you may choose to exclude the champignons from the pizza. But the restaurant has created this pizza with its own recipe. That's why you mostly avoid that restaurant if the pizza dough is shit in your opinion, instead of telling the chef how to set up the dough.
Then you could make your own pizza at home. You have a recipe, but you can vary it. Even though, If it's a special pizza, you couldn't fuck around that much in order to get that special pizza. You couldn't, for example, put meat on that pizza if you would want a meatless pizza. Makes sense.
So, if suddenly a game like Dark Souls tells you that, oh hey, if you had phoned in 3 hours prior to your arrival, you could have told us how we should make the pizza dough, and they'd tell you this right after you've finished that pizza, then fuck them. Especially if it was a shit pizza to begin with. If now for example FallOut 4 told you that it would have become a even more linear cover-shooter, and nobody would have known that, like if everytime you would make a pizza at home, the pizza GeStaPo would arrive at your home to tell you how to make that pizza at gun-point, then I were pretty surprised. And disappointed.
Then you have Cave Story. It's like a chocolate bar. You eat it, it maybe even was a Snickers 10 times as big, it was made of WunderBar and rainbows, done. You wouldn't even think of making one of these at home. How should you know that? That if you perform a special ritual, an owl flies by to drop you the secret recipe to make a Snickers in a micro wave? How should you know that this was possible? CaveStory is a jump'n'run sh'm'up. It's a bit metroidvania, maybe even a bit more. And the differences are no joke, either. New weapons, a new ending. And you had to do such unintuitive shit. You don't expect that. How is one supposed to *even think of that* after 72890239047 jump'n'run sh'm'ups told one otherwise, that there IS ONLY ONE OR TWO ENDINGS, that there IS JUST THIS AND THIS AMOUNT OF PATHES THROUGH THE GAME, and that there IS MAYBE JUST ONE OR TWO REAL SECRETS like the slightly altered ending to Super Metroid, where Samus saved the animals? How should one expect that and anticipate it when it's *SO* illogical?
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TL;DR: If it's in an unexpected genre and totally illogical, as well as significant, it sucks.