I've dabbled a bit with Minecraft and had some fun, but I've always thought it needed more game systems because every session just becomes the same thing over and over.
Have you ever played modded MC? As some of what you suggest sounds very close to a number of mods.
Off the top of my head;
They could add a quest system and expand the village/NPC interaction with text-based dialogue. So for example; doing quests for a village head, anything from helping them remove a monster spawner beneath the village, getting them material to build new houses for their growing population, or finding particular rare items they want for the village. You could even expand the like/dislike system with a sort of good/evil system that determines the direction villagers will go, so they could join up with the pillagers or something or become their enemies. You could have a standing based on how good/evil you are and depending on which could mean certain enemies come after you etc./
It isn't exactly like you described but TekTopia comes close. Best way I can think to explain it is that you're a leader of a village and the idea is to build a working village. So you have to build the buildings (storage, villager houses, trading hall, sentry post, tavern, mine etc.) and assign villagers to each job (farmer, soldier, bard, miner etc). Each villager has some base stats for each role but will learn further, or a new role, by doing that role though if their stats are low they're not very good at it (so a farmer will destroy farm land when harvesting crops and a certain percentage of crops they will fail to harvest until their farming stat increases). As the village grows, you will get attacked by a spectre thing (not pillagers but can't remember what they are called) that brings other mobs with it. There's no good/evil aspect to it that I remember only a happiness stat that effects how motivated they are to work.
Have a "stuff to do" menu that gives you targets and encourages purpose for exploration rather than whimsically wandering around.
A good number of modpacks have a questbook to them which while not strictly a to-do list, some packs you have to work through the quests in order. These can be simply make a specific tool/block/machine or defeat a boss (vanilla bosses and/or mod bosses)
Improve UI and map interface.
I know there's some mods that change the UI though from my experience they're mostly cosmetic rather than function. Though for a map, JourneyMap is arguably the most popular map mod (the map is the corner of your screen and uncovers as you explore, tells you what biome you're in, allows you set waypoints etc.) though there are others too. There's also plugins things like Dynmap that allow you browse the map in your browser.
Add benefits/buffs to advanced cooked meals (like a lesser alchemy) with many ingredients so that eggs, cakes, soups, meals have a purpose.
Sounds like PamsHarvestCraft and the Nutrition! mod. Pams adds about 100 different ingredients (tomato, chilli, cucumber, lettuce, corn, blackberry, strawberry etc.) that you can combine to make better foods (ploughman's lunch, tacos etc.) Combine that with Nutrition! which keeps track of your Grain, Protein, Dairy, Fruit and Vegatable which if you let some of them get too low you start getting de-buffs (hunger, mining fatigue etc.) but keep them all high and you get buffs (Strength, resistance etc.)
Breeding new variants of animals/monsters with special abilities like FF7 chocobo breeding or something.
Expand the mobs and give them different purposes so that they don't just want to kill you. Like the Witch, maybe she wants to steal your max health for a length of time, or she curses you which means you've got to do evil things to villagers and have to goto the Nether to find a cure.
Or add rare Vampires to the game world that could potentially turn you and means you have to feed from NPCs which would add to your good/evil system, also it'd mean you'd have to build a base at a certain depth from the surface to get away from the sun etc.
Mermaids that try to drag you to their underwater lairs.
Flying creatures/demons that can drag you to the Nether (would be freaking terrifying!)
These I'm not so sure on, there are plenty of mods that add mobs, like Sea Sirens, though none that I know of that change their purpose like you're suggesting. I tend to stick to more of the tech mods though so there might be mods that do this as they would feature best in the more rpg/questing style packs.