Extensibility. Official server still doesn't have plugin API and it is closed-source so it can't be modified. Almost everyone uses spigot/bukkit/sponge because vanilla server lacks many features, but these are dirty hacks based on disassembly.
The lua plugin system is well-developed and documented [1] so most plugins could be changed over easily.
- WorldEdit: https://forum.cuberite.org/thread-870.html
- Essentials: https://forum.cuberite.org/thread-1840.html
But also minigames like
- SkyBlock: https://forum.cuberite.org/thread-1508.html
- HungerGames: https://forum.cuberite.org/thread-1456.html
At that point, why not just switch over to Minetest? Given enough work, it could eventually be an attractive and feature-complete clone — and be nicely extensible too.