I agree with almost everything you have said and altho, there are more things I wanna see addressed, this would be a great start. I would also like to add that respec cost, once they add respecs, should not exist until they fix weapon/shield stat requirements as its straight up punishing for new players for not knowing what was not explained to them in the first place, basically, for trying to play and learn the game.
I was thinking about estus flasks as well, and now that I saw ur post I do agree that they should be rechargable on death, and not by interacting with whiper, however, they should also be recharged by slaying enemies, as in, every few enemies killed or something, and maybe with time as well. However, whisper should full heal u when u interact with it, otherwise u r punishing new players for no reason, and it stops mattering once you reach town anyways.
Additionally, all food items being primarly healing items should cease to exist. This is my suggestion for reworking them. You could make a hunger bar that gets filled fully by eating any 2 of them. Add a button to throw up if you wanna switch buffs, animation could last 3+ seconds to not allow exploiting food as healing items on bosses. They would basically be an hour long buffs that slowly decreases in value over time, and once you reach 50% hunger again you can eat another piece of food. If you go with this system cooldown for eating food should be removed, and cooldown for estus flasks should not be implemented to begin with.
Talking about quickitems, oils and vials last for far 2 short of a period, their duration should increase fivefold at the very least. I do not wanna be applying it multiple times through a bossfight.
And there is third point I had to add, when it comes to upgrading sacrament and housing, why doesnt upgrading sawmill, furnance and what not in sacrament upgarde the ones you can place or have already placed in ur house?
Coming to my last idea. All weapons that do plague or heat damage should require faith, while all weapons that do cold or lightning should require intellect to use. Inserting a plague or fire rune should add faith requirement to the item and scalling as well, depending on the items rank. If you wanna keep 1 element per weapon limitation for this to work you would have to remove option to insert gems or runes to an item of wrong elemental type in enchanted weapon with certain element and you could use this same method to limit about of affixes you could roll by enchanting an item with rune of gem of certain element already inserted in it.
Additionally, it would be very cool if dual wield weapons were allowed to have separate extra damage type for each hand, as in, one fire, other plague as affixes, maybe both that belong to the same stat, or even not neccessarly, with halved values of each. I, personally, would enjoy running daggers with fire and plague. Additionally you could introduce certain unique armor gear later on that allows you to do more damage to targets affected by x element.
EDIT: rethinking food system and explained it in a way I think would be the best way to have it in the game
EDIT2: explaing my take on elemental weapons and their scalling