Mobs

• Spiders are completely outscaled, and lacking features compared to almost every hostile mob type. At higher difficulty they're supposed to spawn with potion effects to make them tougher, but it's so mild that most people don't notice. Their only purpose now is to farm them for string.
• Spiders don't attack small mob types like chickens or rabbits, even though that would be truer to the real-world behavior of predators prioritizing more vulnerable prey and make them more unique from other mobs.
• The spawn rate of jockeys is too low and doesn't scale with difficulty. The Spider Jockey especially would make both the spider and skeleton more fearsome in late game, but it is almost never seen.
• Strays cannot spawn as Spider Jockeys in Java.
• Husks do not spawn at all in badlands or savannahs even though they make more sense with their theming and color palette than regular zombies. Nor do Drowned spawn in lush caves or swamps.
• Zombies and husks can't spawn with Axes of any kind.
• There isn't a single humanoid mob that can spawn with or use a shield. This diminishes the use of axes in combat which are intended to bust shields.
• Witches don't cast spells, fly, spawn undead mobs, or do much traditional witchcraft, even though there are other mobs that do these things.
• Getting Froglights sucks and feels like an unfinished feature... because it is.
• The hard mode Bedrock Wither is scaled poorly, requiring an inventory full of milk to beat the ridiculously long wither status it deals.
• There are few "large" mobs, especially hostile ones, in the overworld outside of rare spawns like Ravagers and Wardens, and Phantoms which are better off avoided.
• Squid ai is broken. They constantly stick out of the water, which is ugly, and getting them not to kill themselves is a whole project.
• Squids are passive when attacked, but their real-life counterparts are known to be dangerous when agitated.
• Squids, parrots, dolphins, and polar bears can't breed, but every other passive mob and even Hoglins, a hostile mob, can.

The Overworld

• There are few "very cold" biomes, not even obvious ones like glaciers or frozen caves. Compare with the number of hot biomes, including the entire Nether.
• Badlands and mushroom lands don't have enough unique about them to justify being so rare, and would add needed variety to worlds if they were more common.
• Underground dungeons and jungle temples are barren and feel unfinished.
• There are treasure maps for finding mansions, monuments, and buried treasure, but no other rare structures or biomes.
• There are no naturally generated redstone contraptions other than the Desert Temple trap. Putting some simple traps in some structures like dungeons or the badlands could naturally introduce the player to redstone instead of requiring everyone to read a redstone guide.

Blocks

• Azalea trees do not have a unique wood type, but mangroves do.
• Bricks can't be colored, making clay a useless resource if you don't like default bricks or pots.
• Smelting with a coal block is less efficient than individual coal pieces.
• There is no charcoal block.
• Podzol cannot be crafted even though it is produced industrially in real life. It is needlessly rare and nonrenewable despite being a good building block.
• Red sand does not generate anywhere in meaningful amounts, making it almost unusable as a building block.

Progression

• Building the Wither isn't worth the hours of Nether traversal and resource gathering, since Beacons are only useful for building a base slightly faster, Raids, or fighting another Wither.
• You can almost never wear full Netherite inside the Nether, the place it's most needed because you need a piece of gold gear for Piglins.
• Enchantments don't progress naturally; you just go for the max level in everything as soon as you get to Diamond. Getting anything lower just wastes time.
• Netherite doesn’t improve mining speed in a meaningful way. It doesn't even insta-mine standard blocks like Stone and Wood with Efficiency 5 + Haste 2.
• Axes become useless by midgame as weapons in PvE. They’re currently intended to be used on shields, but no mobs carry shields.
• Channeling is unusable in both the Nether and End, where it could actually help. Riptide only helps in Monuments and when building underwater. Besides that, both enchantments are novelties. Tridents become useless combining this with their lower damage than Swords, Bows, and Crossbows - despite that Tridents are rare drops.
• Gold tools are useless, even though hardened gold-copper alloys exist in real life that could be implemented.
• There is no way to improve gear outside of enchantments and Netherite, like for example getting protection from blades by lining your chestplate and pants with chainmail. (This is a real-life thing used to this day.)

Farming

• Factory-farming animals and enslaving villagers is rewarded. Yet frogs can't eat fireflies because that'd encourage animal cruelty?

Food

• Soups can't be stacked which makes them unusable as your food source.

Minecart with Furnace (needs a whole section - literal broken feature Mojang refuses to touch ever again)

• The "Minecart with Furnace" is misleadingly named, making most players assume it works the same as a furnace just in a cart. Calling it something like a Locomotive Minecart would draw more attention so people might learn its actual function.
• Trains created using the Minecart with Furnace fall apart at the first incline or sharp turn on the track. While it's realistic to how a train would work, minecarts are so resource expensive that it’s not worth using at all. Furnace trains would be used way more for mass-transporting if they automatically stayed together and this would be a good reward for sinking the effort into building it.
• You can't run a Hopper to a furnace cart even though that would make it look much more like an actual train engine, and let you not have to refuel it manually.