Brewing (also features a lock-key system like in zelda dungeons; might be useful for modpack-making)
Stealth (with the exception of the warden, this system is almost nonexistent in vanilla as mobs detect others using a radius instead of lines of sight and sound detection) (1.12)
Weather (Addon of Weather, Storms and Tornadoes)
About
This stack includes all mods I know which question Minecraft Systems and completely reworks them
Usually, those mods aren't considered "vanilla +" because they go too far in rethinking the key systems, as they are often not afraid of questioning concepts which have been established for years;
Sometimes these mods will be seen as going beyond Vanilla+ content, sometimes as something more on the side, depend on the mod and who you ask
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