I do agree that the quests that are required to continue the Main story should either be updated ro Main Quests or given their own category (dunno what would call them).
Key Quests? Gateway Quests?
Off the top of my head those quests are:
Speak to the Villagers (the linchpin for the whole game)
Find The Blacksmith's Dog
Find The Poacher & The Peddler's Fate
Clear The Mill & Flour For The Baker
Journey To The Swamp & Save Your Chap
Clerical Robes & Ring A Bell
Enhanced Fertility Potion
Acorns/Security, Chickens, A Larger Home For Julia, and Growing Up
Transformation, Troublesome Zealots, and Mother And Child In Distress
Not 100% sure you have to do Prove Your Reliability before Beth agrees to a date with you, haven't tested that yet.
Trouble At The Well is debatable. It used to be almost required since EFPs need sacred water, and you'd have to stop making other potions once TATW would trigger to avoid it. Since Daiyu was added you can buy nearly any potion from her and reserve the water for EFPs (and Cure Poison, she doesn't sell those). But with Ancient Chests you can stockpile literally thousands of sacred water doses and not go to the well any more once TATW would trigger, without having to stop making potions yourself.