My least favorite so far was Searching For Answers(Darkspine), but I'm currently on Right from the Gecko(Goldsea) and I have a feeling this is only the beginning.
I don't remember any of the story quests other than the token one (don't like that one) but my least favourite encounter is the trinket one because you have to press two buttons and you don't get food or knuckles
The bugged quests that still show up in perpetuity in a few areas for some reason get old, but there's not much reason to go back to most of those areas once you level past them, at least.
As for a least favorite, well-- it's not one in particular, but a lot of the ch1 missions suffer from artificial slow-downs to pad out their run time, I really hope that design philosophy doesn't continue into Ch2 and beyond. It doesn't really add anything of substance to a story to be drawn out with excessive rng, but it can easily impact enjoyment of it. I also hope they fix the Ch1 quests sticking around bug before they release Ch2. :P
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"Once again I have to bear the burden of having every correct opinion in the world."